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odak.tools

odak.tools

Provides necessary definitions for general tools used across the library.

latex

A class to work with latex documents.

Source code in odak/tools/latex.py 
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class latex():
    """
    A class to work with latex documents.
    """
    def __init__(
                 self,
                 filename
                ):
        """
        Parameters
        ----------
        filename     : str
                       Source filename (i.e. sample.tex).
        """
        self.filename = filename
        self.content = read_text_file(self.filename)
        self.content_type = []
        self.latex_dictionary = [
                                 '\\documentclass',
                                 '\\if',
                                 '\\pdf',
                                 '\\else',
                                 '\\fi',
                                 '\\vgtc',
                                 '\\teaser',
                                 '\\abstract',
                                 '\\CCS',
                                 '\\usepackage',
                                 '\\PassOptionsToPackage',
                                 '\\definecolor',
                                 '\\AtBeginDocument',
                                 '\\providecommand',
                                 '\\setcopyright',
                                 '\\copyrightyear',
                                 '\\acmYear',
                                 '\\citestyle',
                                 '\\newcommand',
                                 '\\acmDOI',
                                 '\\newabbreviation',
                                 '\\global',
                                 '\\begin{document}',
                                 '\\author',
                                 '\\affiliation',
                                 '\\email',
                                 '\\institution',
                                 '\\streetaddress',
                                 '\\city',
                                 '\\country',
                                 '\\postcode',
                                 '\\ccsdesc',
                                 '\\received',
                                 '\\includegraphics',
                                 '\\caption',
                                 '\\centering',
                                 '\\label',
                                 '\\maketitle',
                                 '\\toprule',
                                 '\\multirow',
                                 '\\multicolumn',
                                 '\\cmidrule',
                                 '\\addlinespace',
                                 '\\midrule',
                                 '\\cellcolor',
                                 '\\bibliography',
                                 '}',
                                 '\\title',
                                 '</ccs2012>',
                                 '\\bottomrule',
                                 '<concept>',
                                 '<concept',
                                 '<ccs',
                                 '\\item',
                                 '</concept',
                                 '\\begin{abstract}',
                                 '\\end{abstract}',
                                 '\\endinput',
                                 '\\\\'
                                ]
        self.latex_begin_dictionary = [
                                       '\\begin{figure}',
                                       '\\begin{figure*}',
                                       '\\begin{equation}',
                                       '\\begin{CCSXML}',
                                       '\\begin{teaserfigure}',
                                       '\\begin{table*}',
                                       '\\begin{table}',
                                       '\\begin{gather}',
                                       '\\begin{align}',
                                      ]
        self.latex_end_dictionary = [
                                     '\\end{figure}',
                                     '\\end{figure*}',
                                     '\\end{equation}',
                                     '\\end{CCSXML}',
                                     '\\end{teaserfigure}',
                                     '\\end{table*}',
                                     '\\end{table}',
                                     '\\end{gather}',
                                     '\\end{align}',
                                    ]
        self._label_lines()


    def set_latex_dictonaries(self, begin_dictionary, end_dictionary, syntax_dictionary):
        """
        Set document specific dictionaries so that the lines could be labelled in accordance.


        Parameters
        ----------
        begin_dictionary     : list
                               Pythonic list containing latex syntax for begin commands (i.e. \\begin{align}).
        end_dictionary       : list
                               Pythonic list containing latex syntax for end commands (i.e. \\end{table}).
        syntax_dictionary    : list
                               Pythonic list containing latex syntax (i.e. \\item).

        """
        self.latex_begin_dictionary = begin_dictionary
        self.latex_end_dictionary = end_dictionary
        self.latex_dictionary = syntax_dictionary
        self._label_lines


    def _label_lines(self):
        """
        Internal function for labelling lines.
        """
        content_type_flag = False
        for line_id, line in enumerate(self.content):
            while len(line) > 0 and line[0] == ' ':
                 line = line[1::]
            self.content[line_id] = line
            if len(line) == 0:
                content_type = 'empty'
            elif line[0] == '%':
                content_type = 'comment'
            else:
                content_type = 'text'
            for syntax in self.latex_begin_dictionary:
                if line.find(syntax) != -1:
                    content_type_flag = True
                    content_type = 'latex'
            for syntax in self.latex_dictionary:
                if line.find(syntax) != -1:
                    content_type = 'latex'
            if content_type_flag == True:
                content_type = 'latex'
                for syntax in self.latex_end_dictionary:
                    if line.find(syntax) != -1:
                         content_type_flag = False
            self.content_type.append(content_type)


    def get_line_count(self):
        """
        Definition to get the line count.


        Returns
        -------
        line_count     : int
                         Number of lines in the loaded latex document.
        """
        self.line_count = len(self.content)
        return self.line_count


    def get_line(self, line_id = 0):
        """
        Definition to get a specific line by inputting a line nunber.


        Returns
        ----------
        line           : str
                         Requested line.
        content_type   : str
                         Line's content type (e.g., latex, comment, text).
        """
        line = self.content[line_id]
        content_type = self.content_type[line_id]
        return line, content_type

__init__(filename)

Parameters:

  • filename – 
           Source filename (i.e. sample.tex).
Source code in odak/tools/latex.py 
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def __init__(
             self,
             filename
            ):
    """
    Parameters
    ----------
    filename     : str
                   Source filename (i.e. sample.tex).
    """
    self.filename = filename
    self.content = read_text_file(self.filename)
    self.content_type = []
    self.latex_dictionary = [
                             '\\documentclass',
                             '\\if',
                             '\\pdf',
                             '\\else',
                             '\\fi',
                             '\\vgtc',
                             '\\teaser',
                             '\\abstract',
                             '\\CCS',
                             '\\usepackage',
                             '\\PassOptionsToPackage',
                             '\\definecolor',
                             '\\AtBeginDocument',
                             '\\providecommand',
                             '\\setcopyright',
                             '\\copyrightyear',
                             '\\acmYear',
                             '\\citestyle',
                             '\\newcommand',
                             '\\acmDOI',
                             '\\newabbreviation',
                             '\\global',
                             '\\begin{document}',
                             '\\author',
                             '\\affiliation',
                             '\\email',
                             '\\institution',
                             '\\streetaddress',
                             '\\city',
                             '\\country',
                             '\\postcode',
                             '\\ccsdesc',
                             '\\received',
                             '\\includegraphics',
                             '\\caption',
                             '\\centering',
                             '\\label',
                             '\\maketitle',
                             '\\toprule',
                             '\\multirow',
                             '\\multicolumn',
                             '\\cmidrule',
                             '\\addlinespace',
                             '\\midrule',
                             '\\cellcolor',
                             '\\bibliography',
                             '}',
                             '\\title',
                             '</ccs2012>',
                             '\\bottomrule',
                             '<concept>',
                             '<concept',
                             '<ccs',
                             '\\item',
                             '</concept',
                             '\\begin{abstract}',
                             '\\end{abstract}',
                             '\\endinput',
                             '\\\\'
                            ]
    self.latex_begin_dictionary = [
                                   '\\begin{figure}',
                                   '\\begin{figure*}',
                                   '\\begin{equation}',
                                   '\\begin{CCSXML}',
                                   '\\begin{teaserfigure}',
                                   '\\begin{table*}',
                                   '\\begin{table}',
                                   '\\begin{gather}',
                                   '\\begin{align}',
                                  ]
    self.latex_end_dictionary = [
                                 '\\end{figure}',
                                 '\\end{figure*}',
                                 '\\end{equation}',
                                 '\\end{CCSXML}',
                                 '\\end{teaserfigure}',
                                 '\\end{table*}',
                                 '\\end{table}',
                                 '\\end{gather}',
                                 '\\end{align}',
                                ]
    self._label_lines()

get_line(line_id=0)

Definition to get a specific line by inputting a line nunber.

Returns:

  • line ( str ) –

    Requested line.

  • content_type ( str ) –

    Line's content type (e.g., latex, comment, text).

Source code in odak/tools/latex.py 
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def get_line(self, line_id = 0):
    """
    Definition to get a specific line by inputting a line nunber.


    Returns
    ----------
    line           : str
                     Requested line.
    content_type   : str
                     Line's content type (e.g., latex, comment, text).
    """
    line = self.content[line_id]
    content_type = self.content_type[line_id]
    return line, content_type

get_line_count()

Definition to get the line count.

Returns:

  • line_count ( int ) –

    Number of lines in the loaded latex document.

Source code in odak/tools/latex.py 
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def get_line_count(self):
    """
    Definition to get the line count.


    Returns
    -------
    line_count     : int
                     Number of lines in the loaded latex document.
    """
    self.line_count = len(self.content)
    return self.line_count

set_latex_dictonaries(begin_dictionary, end_dictionary, syntax_dictionary)

Set document specific dictionaries so that the lines could be labelled in accordance.

Parameters:

  • begin_dictionary – 
                   Pythonic list containing latex syntax for begin commands (i.e. \begin{align}).
  • end_dictionary – 
                   Pythonic list containing latex syntax for end commands (i.e. \end{table}).
  • syntax_dictionary – 
                   Pythonic list containing latex syntax (i.e. \item).
Source code in odak/tools/latex.py 
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def set_latex_dictonaries(self, begin_dictionary, end_dictionary, syntax_dictionary):
    """
    Set document specific dictionaries so that the lines could be labelled in accordance.


    Parameters
    ----------
    begin_dictionary     : list
                           Pythonic list containing latex syntax for begin commands (i.e. \\begin{align}).
    end_dictionary       : list
                           Pythonic list containing latex syntax for end commands (i.e. \\end{table}).
    syntax_dictionary    : list
                           Pythonic list containing latex syntax (i.e. \\item).

    """
    self.latex_begin_dictionary = begin_dictionary
    self.latex_end_dictionary = end_dictionary
    self.latex_dictionary = syntax_dictionary
    self._label_lines

markdown

A class to work with markdown documents.

Source code in odak/tools/markdown.py 
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class markdown():
    """
    A class to work with markdown documents.
    """
    def __init__(
                 self,
                 filename
                ):
        """
        Parameters
        ----------
        filename     : str
                       Source filename (i.e. sample.md).
        """
        self.filename = filename
        self.content = read_text_file(self.filename)
        self.content_type = []
        self.markdown_dictionary = [
                                     '#',
                                   ]
        self.markdown_begin_dictionary = [
                                          '```bash',
                                          '```python',
                                          '```',
                                         ]
        self.markdown_end_dictionary = [
                                        '```',
                                       ]
        self._label_lines()


    def set_dictonaries(self, begin_dictionary, end_dictionary, syntax_dictionary):
        """
        Set document specific dictionaries so that the lines could be labelled in accordance.


        Parameters
        ----------
        begin_dictionary     : list
                               Pythonic list containing markdown syntax for beginning of blocks (e.g., code, html).
        end_dictionary       : list
                               Pythonic list containing markdown syntax for end of blocks (e.g., code, html).
        syntax_dictionary    : list
                               Pythonic list containing markdown syntax (i.e. \\item).

        """
        self.markdown_begin_dictionary = begin_dictionary
        self.markdown_end_dictionary = end_dictionary
        self.markdown_dictionary = syntax_dictionary
        self._label_lines


    def _label_lines(self):
        """
        Internal function for labelling lines.
        """
        content_type_flag = False
        for line_id, line in enumerate(self.content):
            while len(line) > 0 and line[0] == ' ':
                 line = line[1::]
            self.content[line_id] = line
            if len(line) == 0:
                content_type = 'empty'
            elif line[0] == '%':
                content_type = 'comment'
            else:
                content_type = 'text'
            for syntax in self.markdown_begin_dictionary:
                if line.find(syntax) != -1:
                    content_type_flag = True
                    content_type = 'markdown'
            for syntax in self.markdown_dictionary:
                if line.find(syntax) != -1:
                    content_type = 'markdown'
            if content_type_flag == True:
                content_type = 'markdown'
                for syntax in self.markdown_end_dictionary:
                    if line.find(syntax) != -1:
                         content_type_flag = False
            self.content_type.append(content_type)


    def get_line_count(self):
        """
        Definition to get the line count.


        Returns
        -------
        line_count     : int
                         Number of lines in the loaded markdown document.
        """
        self.line_count = len(self.content)
        return self.line_count


    def get_line(self, line_id = 0):
        """
        Definition to get a specific line by inputting a line nunber.


        Returns
        ----------
        line           : str
                         Requested line.
        content_type   : str
                         Line's content type (e.g., markdown, comment, text).
        """
        line = self.content[line_id]
        content_type = self.content_type[line_id]
        return line, content_type

__init__(filename)

Parameters:

  • filename – 
           Source filename (i.e. sample.md).
Source code in odak/tools/markdown.py 
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def __init__(
             self,
             filename
            ):
    """
    Parameters
    ----------
    filename     : str
                   Source filename (i.e. sample.md).
    """
    self.filename = filename
    self.content = read_text_file(self.filename)
    self.content_type = []
    self.markdown_dictionary = [
                                 '#',
                               ]
    self.markdown_begin_dictionary = [
                                      '```bash',
                                      '```python',
                                      '```',
                                     ]
    self.markdown_end_dictionary = [
                                    '```',
                                   ]
    self._label_lines()

get_line(line_id=0)

Definition to get a specific line by inputting a line nunber.

Returns:

  • line ( str ) –

    Requested line.

  • content_type ( str ) –

    Line's content type (e.g., markdown, comment, text).

Source code in odak/tools/markdown.py 
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def get_line(self, line_id = 0):
    """
    Definition to get a specific line by inputting a line nunber.


    Returns
    ----------
    line           : str
                     Requested line.
    content_type   : str
                     Line's content type (e.g., markdown, comment, text).
    """
    line = self.content[line_id]
    content_type = self.content_type[line_id]
    return line, content_type

get_line_count()

Definition to get the line count.

Returns:

  • line_count ( int ) –

    Number of lines in the loaded markdown document.

Source code in odak/tools/markdown.py 
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def get_line_count(self):
    """
    Definition to get the line count.


    Returns
    -------
    line_count     : int
                     Number of lines in the loaded markdown document.
    """
    self.line_count = len(self.content)
    return self.line_count

set_dictonaries(begin_dictionary, end_dictionary, syntax_dictionary)

Set document specific dictionaries so that the lines could be labelled in accordance.

Parameters:

  • begin_dictionary – 
                   Pythonic list containing markdown syntax for beginning of blocks (e.g., code, html).
  • end_dictionary – 
                   Pythonic list containing markdown syntax for end of blocks (e.g., code, html).
  • syntax_dictionary – 
                   Pythonic list containing markdown syntax (i.e. \item).
Source code in odak/tools/markdown.py 
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def set_dictonaries(self, begin_dictionary, end_dictionary, syntax_dictionary):
    """
    Set document specific dictionaries so that the lines could be labelled in accordance.


    Parameters
    ----------
    begin_dictionary     : list
                           Pythonic list containing markdown syntax for beginning of blocks (e.g., code, html).
    end_dictionary       : list
                           Pythonic list containing markdown syntax for end of blocks (e.g., code, html).
    syntax_dictionary    : list
                           Pythonic list containing markdown syntax (i.e. \\item).

    """
    self.markdown_begin_dictionary = begin_dictionary
    self.markdown_end_dictionary = end_dictionary
    self.markdown_dictionary = syntax_dictionary
    self._label_lines

batch_of_rays(entry, exit)

Definition to generate a batch of rays with given entry point(s) and exit point(s). Note that the mapping is one to one, meaning nth item in your entry points list will exit from nth item in your exit list and generate that particular ray. Note that you can have a combination like nx3 points for entry or exit and 1 point for entry or exit. But if you have multiple points both for entry and exit, the number of points have to be same both for entry and exit.

Parameters:

  • entry – 
         Either a single point with size of 3 or multiple points with the size of nx3.
  • exit – 
         Either a single point with size of 3 or multiple points with the size of nx3.

Returns:

  • rays ( ndarray ) –

    Generated batch of rays.

Source code in odak/tools/sample.py 
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def batch_of_rays(entry, exit):
    """
    Definition to generate a batch of rays with given entry point(s) and exit point(s). Note that the mapping is one to one, meaning nth item in your entry points list will exit from nth item in your exit list and generate that particular ray. Note that you can have a combination like nx3 points for entry or exit and 1 point for entry or exit. But if you have multiple points both for entry and exit, the number of points have to be same both for entry and exit.

    Parameters
    ----------
    entry      : ndarray
                 Either a single point with size of 3 or multiple points with the size of nx3.
    exit       : ndarray
                 Either a single point with size of 3 or multiple points with the size of nx3.

    Returns
    ----------
    rays       : ndarray
                 Generated batch of rays.
    """
    norays = np.array([0, 0])
    if len(entry.shape) == 1:
        entry = entry.reshape((1, 3))
    if len(exit.shape) == 1:
        exit = exit.reshape((1, 3))
    norays = np.amax(np.asarray([entry.shape[0], exit.shape[0]]))
    if norays > exit.shape[0]:
        exit = np.repeat(exit, norays, axis=0)
    elif norays > entry.shape[0]:
        entry = np.repeat(entry, norays, axis=0)
    rays = []
    norays = int(norays)
    for i in range(norays):
        rays.append(
            create_ray_from_two_points(
                entry[i],
                exit[i]
            )
        )
    rays = np.asarray(rays)
    return rays

blur_gaussian(field, kernel_length=[21, 21], nsigma=[3, 3])

A definition to blur a field using a Gaussian kernel.

Parameters:

  • field – 
            MxN field.
  • kernel_length (list, default: [21, 21] ) – 
            Length of the Gaussian kernel along X and Y axes.
  • nsigma – 
            Sigma of the Gaussian kernel along X and Y axes.

Returns:

  • blurred_field ( ndarray ) –

    Blurred field.

Source code in odak/tools/matrix.py 
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def blur_gaussian(field, kernel_length=[21, 21], nsigma=[3, 3]):
    """
    A definition to blur a field using a Gaussian kernel.

    Parameters
    ----------
    field         : ndarray
                    MxN field.
    kernel_length : list
                    Length of the Gaussian kernel along X and Y axes.
    nsigma        : list
                    Sigma of the Gaussian kernel along X and Y axes.

    Returns
    ----------
    blurred_field : ndarray
                    Blurred field.
    """
    kernel = generate_2d_gaussian(kernel_length, nsigma)
    kernel = zero_pad(kernel, field.shape)
    blurred_field = convolve2d(field, kernel)
    blurred_field = blurred_field/np.amax(blurred_field)
    return blurred_field

box_volume_sample(no=[10, 10, 10], size=[100.0, 100.0, 100.0], center=[0.0, 0.0, 0.0], angles=[0.0, 0.0, 0.0])

Definition to generate samples in a box volume.

Parameters:

  • no – 
          Number of samples.
  • size – 
          Physical size of the volume.
  • center – 
          Center location of the volume.
  • angles – 
          Tilt of the volume.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def box_volume_sample(no=[10, 10, 10], size=[100., 100., 100.], center=[0., 0., 0.], angles=[0., 0., 0.]):
    """
    Definition to generate samples in a box volume.

    Parameters
    ----------
    no          : list
                  Number of samples.
    size        : list
                  Physical size of the volume.
    center      : list
                  Center location of the volume.
    angles      : list
                  Tilt of the volume.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.zeros((no[0], no[1], no[2], 3))
    x, y, z = np.mgrid[0:no[0], 0:no[1], 0:no[2]]
    step = [
        size[0]/no[0],
        size[1]/no[1],
        size[2]/no[2]
    ]
    samples[:, :, :, 0] = x*step[0]+step[0]/2.-size[0]/2.
    samples[:, :, :, 1] = y*step[1]+step[1]/2.-size[1]/2.
    samples[:, :, :, 2] = z*step[2]+step[2]/2.-size[2]/2.
    samples = samples.reshape(
        (samples.shape[0]*samples.shape[1]*samples.shape[2], samples.shape[3]))
    samples = rotate_points(samples, angles=angles, offset=center)
    return samples

check_directory(directory)

Definition to check if a directory exist. If it doesn't exist, this definition will create one.

Parameters:

  • directory – 
            Full directory path.
Source code in odak/tools/file.py 
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def check_directory(directory):
    """
    Definition to check if a directory exist. If it doesn't exist, this definition will create one.


    Parameters
    ----------
    directory     : str
                    Full directory path.
    """
    if not os.path.exists(expanduser(directory)):
        os.makedirs(expanduser(directory))
        return False
    return True

circular_sample(no=[10, 10], radius=10.0, center=[0.0, 0.0, 0.0], angles=[0.0, 0.0, 0.0])

Definition to generate samples inside a circle over a surface.

Parameters:

  • no – 
          Number of samples.
  • radius – 
          Radius of the circle.
  • center – 
          Center location of the surface.
  • angles – 
          Tilt of the surface.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def circular_sample(no=[10, 10], radius=10., center=[0., 0., 0.], angles=[0., 0., 0.]):
    """
    Definition to generate samples inside a circle over a surface.

    Parameters
    ----------
    no          : list
                  Number of samples.
    radius      : float
                  Radius of the circle.
    center      : list
                  Center location of the surface.
    angles      : list
                  Tilt of the surface.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.zeros((no[0]+1, no[1]+1, 3))
    r_angles, r = np.mgrid[0:no[0]+1, 0:no[1]+1]
    r = r/np.amax(r)*radius
    r_angles = r_angles/np.amax(r_angles)*np.pi*2
    samples[:, :, 0] = r*np.cos(r_angles)
    samples[:, :, 1] = r*np.sin(r_angles)
    samples = samples[1:no[0]+1, 1:no[1]+1, :]
    samples = samples.reshape(
        (samples.shape[0]*samples.shape[1], samples.shape[2]))
    samples = rotate_points(samples, angles=angles, offset=center)
    return samples

circular_uniform_random_sample(no=[10, 50], radius=10.0, center=[0.0, 0.0, 0.0], angles=[0.0, 0.0, 0.0])

Definition to generate sample inside a circle uniformly but randomly.

Parameters:

  • no – 
          Number of samples.
  • radius – 
          Radius of the circle.
  • center – 
          Center location of the surface.
  • angles – 
          Tilt of the surface.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def circular_uniform_random_sample(no=[10, 50], radius=10., center=[0., 0., 0.], angles=[0., 0., 0.]):
    """ 
    Definition to generate sample inside a circle uniformly but randomly.

    Parameters
    ----------
    no          : list
                  Number of samples.
    radius      : float
                  Radius of the circle.
    center      : list
                  Center location of the surface.
    angles      : list
                  Tilt of the surface.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.empty((0, 3))
    rs = np.sqrt(np.random.uniform(0, 1, no[0]))
    angs = np.random.uniform(0, 2*np.pi, no[1])
    for i in rs:
        for angle in angs:
            r = radius*i
            point = np.array(
                [float(r*np.cos(angle)), float(r*np.sin(angle)), 0])
            samples = np.vstack((samples, point))
    samples = rotate_points(samples, angles=angles, offset=center)
    return samples

circular_uniform_sample(no=[10, 50], radius=10.0, center=[0.0, 0.0, 0.0], angles=[0.0, 0.0, 0.0])

Definition to generate sample inside a circle uniformly.

Parameters:

  • no – 
          Number of samples.
  • radius – 
          Radius of the circle.
  • center – 
          Center location of the surface.
  • angles – 
          Tilt of the surface.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def circular_uniform_sample(no=[10, 50], radius=10., center=[0., 0., 0.], angles=[0., 0., 0.]):
    """
    Definition to generate sample inside a circle uniformly.

    Parameters
    ----------
    no          : list
                  Number of samples.
    radius      : float
                  Radius of the circle.
    center      : list
                  Center location of the surface.
    angles      : list
                  Tilt of the surface.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.empty((0, 3))
    for i in range(0, no[0]):
        r = i/no[0]*radius
        ang_no = no[1]*i/no[0]
        for j in range(0, int(no[1]*i/no[0])):
            angle = j/ang_no*2*np.pi
            point = np.array(
                [float(r*np.cos(angle)), float(r*np.sin(angle)), 0])
            samples = np.vstack((samples, point))
    samples = rotate_points(samples, angles=angles, offset=center)
    return samples

closest_point_to_a_ray(point, ray)

Definition to calculate the point on a ray that is closest to given point.

Parameters:

  • point – 
            Given point in X,Y,Z.
  • ray – 
            Given ray.

Returns:

  • closest_point ( ndarray ) –

    Calculated closest point.

Source code in odak/tools/vector.py 
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def closest_point_to_a_ray(point, ray):
    """
    Definition to calculate the point on a ray that is closest to given point.

    Parameters
    ----------
    point         : list
                    Given point in X,Y,Z.
    ray           : ndarray
                    Given ray.

    Returns
    ---------
    closest_point : ndarray
                    Calculated closest point.
    """
    from odak.raytracing import propagate_a_ray
    if len(ray.shape) == 2:
        ray = ray.reshape((1, 2, 3))
    p0 = ray[:, 0]
    p1 = propagate_a_ray(ray, 1.)
    if len(p1.shape) == 2:
        p1 = p1.reshape((1, 2, 3))
    p1 = p1[:, 0]
    p1 = p1.reshape(3)
    p0 = p0.reshape(3)
    point = point.reshape(3)
    closest_distance = -np.dot((p0-point), (p1-p0))/np.sum((p1-p0)**2)
    closest_point = propagate_a_ray(ray, closest_distance)[0]
    return closest_point

convert_bytes(num)

A definition to convert bytes to semantic scheme (MB,GB or alike). Inspired from https://stackoverflow.com/questions/2104080/how-can-i-check-file-size-in-python#2104083.

Parameters:

  • num – 
         Size in bytes

Returns:

  • num ( float ) –

    Size in new unit.

  • x ( str ) –

    New unit bytes, KB, MB, GB or TB.

Source code in odak/tools/file.py 
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def convert_bytes(num):
    """
    A definition to convert bytes to semantic scheme (MB,GB or alike). Inspired from https://stackoverflow.com/questions/2104080/how-can-i-check-file-size-in-python#2104083.


    Parameters
    ----------
    num        : float
                 Size in bytes


    Returns
    ----------
    num        : float
                 Size in new unit.
    x          : str
                 New unit bytes, KB, MB, GB or TB.
    """
    for x in ['bytes', 'KB', 'MB', 'GB', 'TB']:
        if num < 1024.0:
            return num, x
        num /= 1024.0
    return None, None

convert_to_numpy(a)

A definition to convert Torch to Numpy.

Parameters:

  • a – 
         Input Torch array.

Returns:

  • b ( ndarray ) –

    Converted array.

Source code in odak/tools/conversions.py 
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def convert_to_numpy(a):
    """
    A definition to convert Torch to Numpy.

    Parameters
    ----------
    a          : torch.Tensor
                 Input Torch array.

    Returns
    ----------
    b          : numpy.ndarray
                 Converted array.
    """
    b = a.to('cpu').detach().numpy()
    return b

convert_to_torch(a, grad=True)

A definition to convert Numpy arrays to Torch.

Parameters:

  • a – 
         Input Numpy array.
  • grad – 
         Set if the converted array requires gradient.

Returns:

  • c ( Tensor ) –

    Converted array.

Source code in odak/tools/conversions.py 
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def convert_to_torch(a, grad=True):
    """
    A definition to convert Numpy arrays to Torch.

    Parameters
    ----------
    a          : ndarray
                 Input Numpy array.
    grad       : bool
                 Set if the converted array requires gradient.

    Returns
    ----------
    c          : torch.Tensor
                 Converted array.
    """
    b = np.copy(a)
    c = torch.from_numpy(b)
    c.requires_grad_(grad)
    return c

convolve2d(field, kernel)

Definition to convolve a field with a kernel by multiplying in frequency space.

Parameters:

  • field – 
          Input field with MxN shape.
  • kernel – 
          Input kernel with MxN shape.

Returns:

  • new_field ( ndarray ) –

    Convolved field.

Source code in odak/tools/matrix.py 
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def convolve2d(field, kernel):
    """
    Definition to convolve a field with a kernel by multiplying in frequency space.

    Parameters
    ----------
    field       : ndarray
                  Input field with MxN shape.
    kernel      : ndarray
                  Input kernel with MxN shape.

    Returns
    ----------
    new_field   : ndarray
                  Convolved field.
    """
    fr = np.fft.fft2(field)
    fr2 = np.fft.fft2(np.flipud(np.fliplr(kernel)))
    m, n = fr.shape
    new_field = np.real(np.fft.ifft2(fr*fr2))
    new_field = np.roll(new_field, int(-m/2+1), axis=0)
    new_field = np.roll(new_field, int(-n/2+1), axis=1)
    return new_field

copy_file(source, destination, follow_symlinks=True)

Definition to copy a file from one location to another.

Parameters:

  • source – 
              Source filename.
  • destination – 
              Destination filename.
  • follow_symlinks (bool, default: True ) – 
              Set to True to follow the source of symbolic links.
Source code in odak/tools/file.py 
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def copy_file(source, destination, follow_symlinks = True):
    """
    Definition to copy a file from one location to another.



    Parameters
    ----------
    source          : str
                      Source filename.
    destination     : str
                      Destination filename.
    follow_symlinks : bool
                      Set to True to follow the source of symbolic links.
    """
    return shutil.copyfile(
                           expanduser(source),
                           expanduser(source),
                           follow_symlinks = follow_symlinks
                          )

create_empty_list(dimensions=[1, 1])

A definition to create an empty Pythonic list.

Parameters:

  • dimensions – 
           Dimensions of the list to be created.

Returns:

  • new_list ( list ) –

    New empty list.

Source code in odak/tools/matrix.py 
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def create_empty_list(dimensions = [1, 1]):
    """
    A definition to create an empty Pythonic list.

    Parameters
    ----------
    dimensions   : list
                   Dimensions of the list to be created.

    Returns
    -------
    new_list     : list
                   New empty list.
    """
    new_list = 0
    for n in reversed(dimensions):
        new_list = [new_list] * n
    return new_list

create_ray_from_two_points(x0y0z0, x1y1z1)

Definition to create a ray from two given points. Note that both inputs must match in shape.

Parameters:

  • x0y0z0 – 
           List that contains X,Y and Z start locations of a ray (3). It can also be a list of points as well (mx3). This is the starting point.
  • x1y1z1 – 
           List that contains X,Y and Z ending locations of a ray (3). It can also be a list of points as well (mx3). This is the end point.

Returns:

  • ray ( ndarray ) –

    Array that contains starting points and cosines of a created ray.

Source code in odak/raytracing/ray.py 
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def create_ray_from_two_points(x0y0z0, x1y1z1):
    """
    Definition to create a ray from two given points. Note that both inputs must match in shape.

    Parameters
    ----------
    x0y0z0       : list
                   List that contains X,Y and Z start locations of a ray (3). It can also be a list of points as well (mx3). This is the starting point.
    x1y1z1       : list
                   List that contains X,Y and Z ending locations of a ray (3). It can also be a list of points as well (mx3). This is the end point.

    Returns
    ----------
    ray          : ndarray
                   Array that contains starting points and cosines of a created ray.
    """
    x0y0z0 = np.asarray(x0y0z0, dtype=np.float64)
    x1y1z1 = np.asarray(x1y1z1, dtype=np.float64)
    if len(x0y0z0.shape) == 1:
        x0y0z0 = x0y0z0.reshape((1, 3))
    if len(x1y1z1.shape) == 1:
        x1y1z1 = x1y1z1.reshape((1, 3))
    xdiff = x1y1z1[:, 0] - x0y0z0[:, 0]
    ydiff = x1y1z1[:, 1] - x0y0z0[:, 1]
    zdiff = x1y1z1[:, 2] - x0y0z0[:, 2]
    s = np.sqrt(xdiff ** 2 + ydiff ** 2 + zdiff ** 2)
    s[s == 0] = np.nan
    cosines = np.zeros((xdiff.shape[0], 3))
    cosines[:, 0] = xdiff/s
    cosines[:, 1] = ydiff/s
    cosines[:, 2] = zdiff/s
    ray = np.zeros((xdiff.shape[0], 2, 3), dtype=np.float64)
    ray[:, 0] = x0y0z0
    ray[:, 1] = cosines
    if ray.shape[0] == 1:
        ray = ray.reshape((2, 3))
    return ray

crop_center(field, size=None)

Definition to crop the center of a field with 2Mx2N size. The outcome is a MxN array.

Parameters:

  • field – 
          Input field 2Mx2N array.

Returns:

  • cropped ( ndarray ) –

    Cropped version of the input field.

Source code in odak/tools/matrix.py 
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def crop_center(field, size=None):
    """
    Definition to crop the center of a field with 2Mx2N size. The outcome is a MxN array.

    Parameters
    ----------
    field       : ndarray
                  Input field 2Mx2N array.

    Returns
    ----------
    cropped     : ndarray
                  Cropped version of the input field.
    """
    if type(size) == type(None):
        qx = int(np.ceil(field.shape[0])/4)
        qy = int(np.ceil(field.shape[1])/4)
        cropped = np.copy(field[qx:3*qx, qy:3*qy])
    else:
        cx = int(np.ceil(field.shape[0]/2))
        cy = int(np.ceil(field.shape[1]/2))
        hx = int(np.ceil(size[0]/2))
        hy = int(np.ceil(size[1]/2))
        cropped = np.copy(field[cx-hx:cx+hx, cy-hy:cy+hy])
    return cropped

cross_product(vector1, vector2)

Definition to cross product two vectors and return the resultant vector. Used method described under: http://en.wikipedia.org/wiki/Cross_product

Parameters:

  • vector1 – 
           A vector/ray.
  • vector2 – 
           A vector/ray.

Returns:

  • ray ( ndarray ) –

    Array that contains starting points and cosines of a created ray.

Source code in odak/tools/vector.py 
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def cross_product(vector1, vector2):
    """
    Definition to cross product two vectors and return the resultant vector. Used method described under: http://en.wikipedia.org/wiki/Cross_product

    Parameters
    ----------
    vector1      : ndarray
                   A vector/ray.
    vector2      : ndarray
                   A vector/ray.

    Returns
    ----------
    ray          : ndarray
                   Array that contains starting points and cosines of a created ray.
    """
    angle = np.cross(vector1[1].T, vector2[1].T)
    angle = np.asarray(angle)
    ray = np.array([vector1[0], angle], dtype=np.float32)
    return ray

distance_between_point_clouds(points0, points1)

A definition to find distance between every point in one cloud to other points in the other point cloud.

Parameters:

  • points0 – 
          Mx3 points.
  • points1 – 
          Nx3 points.

Returns:

  • distances ( ndarray ) –

    MxN distances.

Source code in odak/tools/vector.py 
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def distance_between_point_clouds(points0, points1):
    """
    A definition to find distance between every point in one cloud to other points in the other point cloud.
    Parameters
    ----------
    points0     : ndarray
                  Mx3 points.
    points1     : ndarray
                  Nx3 points.

    Returns
    ----------
    distances   : ndarray
                  MxN distances.
    """
    c = points1.reshape((1, points1.shape[0], points1.shape[1]))
    a = np.repeat(c, points0.shape[0], axis=0)
    b = points0.reshape((points0.shape[0], 1, points0.shape[1]))
    b = np.repeat(b, a.shape[1], axis=1)
    distances = np.sqrt(np.sum((a-b)**2, axis=2))
    return distances

distance_between_two_points(point1, point2)

Definition to calculate distance between two given points.

Parameters:

  • point1 – 
          First point in X,Y,Z.
  • point2 – 
          Second point in X,Y,Z.

Returns:

  • distance ( float ) –

    Distance in between given two points.

Source code in odak/tools/vector.py 
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def distance_between_two_points(point1, point2):
    """
    Definition to calculate distance between two given points.

    Parameters
    ----------
    point1      : list
                  First point in X,Y,Z.
    point2      : list
                  Second point in X,Y,Z.

    Returns
    ----------
    distance    : float
                  Distance in between given two points.
    """
    point1 = np.asarray(point1)
    point2 = np.asarray(point2)
    if len(point1.shape) == 1 and len(point2.shape) == 1:
        distance = np.sqrt(np.sum((point1-point2)**2))
    elif len(point1.shape) == 2 or len(point2.shape) == 2:
        distance = np.sqrt(np.sum((point1-point2)**2, axis=1))
    return distance

expanduser(filename)

Definition to decode filename using namespaces and shortcuts.

Parameters:

  • filename – 
            Filename.

Returns:

  • new_filename ( str ) –

    Filename.

Source code in odak/tools/file.py 
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def expanduser(filename):
    """
    Definition to decode filename using namespaces and shortcuts.


    Parameters
    ----------
    filename      : str
                    Filename.


    Returns
    -------
    new_filename  : str
                    Filename.
    """
    new_filename = os.path.expanduser(filename)
    return new_filename

generate_2d_gaussian(kernel_length=[21, 21], nsigma=[3, 3])

Generate 2D Gaussian kernel. Inspired from https://stackoverflow.com/questions/29731726/how-to-calculate-a-gaussian-kernel-matrix-efficiently-in-numpy

Parameters:

  • kernel_length (list, default: [21, 21] ) – 
            Length of the Gaussian kernel along X and Y axes.
  • nsigma – 
            Sigma of the Gaussian kernel along X and Y axes.

Returns:

  • kernel_2d ( ndarray ) –

    Generated Gaussian kernel.

Source code in odak/tools/matrix.py 
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def generate_2d_gaussian(kernel_length=[21, 21], nsigma=[3, 3]):
    """
    Generate 2D Gaussian kernel. Inspired from https://stackoverflow.com/questions/29731726/how-to-calculate-a-gaussian-kernel-matrix-efficiently-in-numpy

    Parameters
    ----------
    kernel_length : list
                    Length of the Gaussian kernel along X and Y axes.
    nsigma        : list
                    Sigma of the Gaussian kernel along X and Y axes.

    Returns
    ----------
    kernel_2d     : ndarray
                    Generated Gaussian kernel.
    """
    x = np.linspace(-nsigma[0], nsigma[0], kernel_length[0]+1)
    y = np.linspace(-nsigma[1], nsigma[1], kernel_length[1]+1)
    xx, yy = np.meshgrid(x, y)
    kernel_2d = np.exp(-0.5*(np.square(xx) /
                       np.square(nsigma[0]) + np.square(yy)/np.square(nsigma[1])))
    kernel_2d = kernel_2d/kernel_2d.sum()
    return kernel_2d

generate_bandlimits(size=[512, 512], levels=9)

A definition to calculate octaves used in bandlimiting frequencies in the frequency domain.

Parameters:

  • size – 
         Size of each mask in octaves.

Returns:

  • masks ( ndarray ) –

    Masks (Octaves).

Source code in odak/tools/matrix.py 
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def generate_bandlimits(size=[512, 512], levels=9):
    """
    A definition to calculate octaves used in bandlimiting frequencies in the frequency domain.

    Parameters
    ----------
    size       : list
                 Size of each mask in octaves.

    Returns
    ----------
    masks      : ndarray
                 Masks (Octaves).
    """
    masks = np.zeros((levels, size[0], size[1]))
    cx = int(size[0]/2)
    cy = int(size[1]/2)
    for i in range(0, masks.shape[0]):
        deltax = int((size[0])/(2**(i+1)))
        deltay = int((size[1])/(2**(i+1)))
        masks[
            i,
            cx-deltax:cx+deltax,
            cy-deltay:cy+deltay
        ] = 1.
        masks[
            i,
            int(cx-deltax/2.):int(cx+deltax/2.),
            int(cy-deltay/2.):int(cy+deltay/2.)
        ] = 0.
    masks = np.asarray(masks)
    return masks

grid_sample(no=[10, 10], size=[100.0, 100.0], center=[0.0, 0.0, 0.0], angles=[0.0, 0.0, 0.0])

Definition to generate samples over a surface.

Parameters:

  • no – 
          Number of samples.
  • size – 
          Physical size of the surface.
  • center – 
          Center location of the surface.
  • angles – 
          Tilt of the surface.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def grid_sample(no=[10, 10], size=[100., 100.], center=[0., 0., 0.], angles=[0., 0., 0.]):
    """
    Definition to generate samples over a surface.

    Parameters
    ----------
    no          : list
                  Number of samples.
    size        : list
                  Physical size of the surface.
    center      : list
                  Center location of the surface.
    angles      : list
                  Tilt of the surface.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.zeros((no[0], no[1], 3))
    step = [
        size[0]/(no[0]-1),
        size[1]/(no[1]-1)
    ]
    x, y = np.mgrid[0:no[0], 0:no[1]]
    samples[:, :, 0] = x*step[0]-size[0]/2.
    samples[:, :, 1] = y*step[1]-size[1]/2.
    samples = samples.reshape(
        (samples.shape[0]*samples.shape[1], samples.shape[2]))
    samples = rotate_points(samples, angles=angles, offset=center)
    return samples

list_files(path, key='*.*', recursive=True)

Definition to list files in a given path with a given key.

Parameters:

  • path – 
          Path to a folder.
  • key – 
          Key used for scanning a path.
  • recursive – 
          If set True, scan the path recursively.

Returns:

  • files_list ( ndarray ) –

    list of files found in a given path.

Source code in odak/tools/file.py 
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def list_files(path, key = '*.*', recursive = True):
    """
    Definition to list files in a given path with a given key.


    Parameters
    ----------
    path        : str
                  Path to a folder.
    key         : str
                  Key used for scanning a path.
    recursive   : bool
                  If set True, scan the path recursively.


    Returns
    ----------
    files_list  : ndarray
                  list of files found in a given path.
    """
    if recursive == True:
        search_result = pathlib.Path(expanduser(path)).rglob(key)
    elif recursive == False:
        search_result = pathlib.Path(expanduser(path)).glob(key)
    files_list = []
    for item in search_result:
        files_list.append(str(item))
    files_list = sorted(files_list)
    return files_list

load_dictionary(filename)

Definition to load a dictionary (JSON) file.

Parameters:

  • filename – 
            Filename.

Returns:

  • settings ( dict ) –

    Dictionary read from the file.

Source code in odak/tools/file.py 
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def load_dictionary(filename):
    """
    Definition to load a dictionary (JSON) file.


    Parameters
    ----------
    filename      : str
                    Filename.


    Returns
    ----------
    settings      : dict
                    Dictionary read from the file.

    """
    settings = json.load(open(expanduser(filename)))
    return settings

load_image(fn, normalizeby=0.0, torch_style=False)

Definition to load an image from a given location as a Numpy array.

Parameters:

  • fn – 
           Filename.
  • normalizeby – 
           Value to to normalize images with. Default value of zero will lead to no normalization.
  • torch_style – 
           If set True, it will load an image mxnx3 as 3xmxn.

Returns:

  • image ( ndarray ) –

    Image loaded as a Numpy array.

Source code in odak/tools/file.py 
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def load_image(fn, normalizeby = 0., torch_style = False):
    """ 
    Definition to load an image from a given location as a Numpy array.


    Parameters
    ----------
    fn           : str
                   Filename.
    normalizeby  : float
                   Value to to normalize images with. Default value of zero will lead to no normalization.
    torch_style  : bool
                   If set True, it will load an image mxnx3 as 3xmxn.


    Returns
    ----------
    image        :  ndarray
                    Image loaded as a Numpy array.

    """
    image = cv2.imread(expanduser(fn), cv2.IMREAD_UNCHANGED)
    if isinstance(image, type(None)):
         logging.warning('Image not properly loaded. Check filename or image type.')    
         sys.exit()
    if len(image.shape) > 2:
        new_image = np.copy(image)
        new_image[:, :, 0] = image[:, :, 2]
        new_image[:, :, 2] = image[:, :, 0]
        image = new_image
    if normalizeby != 0.:
        image = image * 1. / normalizeby
    if torch_style == True and len(image.shape) > 2:
        image = np.moveaxis(image, -1, 0)
    return image.astype(float)

nufft2(field, fx, fy, size=None, sign=1, eps=10 ** -12)

A definition to take 2D Non-Uniform Fast Fourier Transform (NUFFT).

Parameters:

  • field – 
          Input field.
  • fx – 
          Frequencies along x axis.
  • fy – 
          Frequencies along y axis.
  • size – 
          Size.
  • sign – 
          Sign of the exponential used in NUFFT kernel.
  • eps – 
          Accuracy of NUFFT.

Returns:

  • result ( ndarray ) –

    Inverse NUFFT of the input field.

Source code in odak/tools/matrix.py 
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def nufft2(field, fx, fy, size=None, sign=1, eps=10**(-12)):
    """
    A definition to take 2D Non-Uniform Fast Fourier Transform (NUFFT).

    Parameters
    ----------
    field       : ndarray
                  Input field.
    fx          : ndarray
                  Frequencies along x axis.
    fy          : ndarray
                  Frequencies along y axis.
    size        : list
                  Size.
    sign        : float
                  Sign of the exponential used in NUFFT kernel.
    eps         : float
                  Accuracy of NUFFT.

    Returns
    ----------
    result      : ndarray
                  Inverse NUFFT of the input field.
    """
    try:
        import finufft
    except:
        print('odak.tools.nufft2 requires finufft to be installed: pip install finufft')
    image = np.copy(field).astype(np.complex128)
    result = finufft.nufft2d2(
        fx.flatten(), fy.flatten(), image, eps=eps, isign=sign)
    if type(size) == type(None):
        result = result.reshape(field.shape)
    else:
        result = result.reshape(size)
    return result

nuifft2(field, fx, fy, size=None, sign=1, eps=10 ** -12)

A definition to take 2D Adjoint Non-Uniform Fast Fourier Transform (NUFFT).

Parameters:

  • field – 
          Input field.
  • fx – 
          Frequencies along x axis.
  • fy – 
          Frequencies along y axis.
  • size – 
          Shape of the NUFFT calculated for an input field.
  • sign – 
          Sign of the exponential used in NUFFT kernel.
  • eps – 
          Accuracy of NUFFT.

Returns:

  • result ( ndarray ) –

    NUFFT of the input field.

Source code in odak/tools/matrix.py 
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def nuifft2(field, fx, fy, size=None, sign=1, eps=10**(-12)):
    """
    A definition to take 2D Adjoint Non-Uniform Fast Fourier Transform (NUFFT).

    Parameters
    ----------
    field       : ndarray
                  Input field.
    fx          : ndarray
                  Frequencies along x axis.
    fy          : ndarray
                  Frequencies along y axis.
    size        : list or ndarray
                  Shape of the NUFFT calculated for an input field.
    sign        : float
                  Sign of the exponential used in NUFFT kernel.
    eps         : float
                  Accuracy of NUFFT.

    Returns
    ----------
    result      : ndarray
                  NUFFT of the input field.
    """
    try:
        import finufft
    except:
        print('odak.tools.nuifft2 requires finufft to be installed: pip install finufft')
    image = np.copy(field).astype(np.complex128)
    if type(size) == type(None):
        result = finufft.nufft2d1(
            fx.flatten(),
            fy.flatten(),
            image.flatten(),
            image.shape,
            eps=eps,
            isign=sign
        )
    else:
        result = finufft.nufft2d1(
            fx.flatten(),
            fy.flatten(),
            image.flatten(),
            (size[0], size[1]),
            eps=eps,
            isign=sign
        )
    result = np.asarray(result)
    return result

point_to_ray_distance(point, ray_point_0, ray_point_1)

Definition to find point's closest distance to a line represented with two points.

Parameters:

  • point – 
          Point to be tested.
  • ray_point_0 (ndarray) – 
          First point to represent a line.
  • ray_point_1 (ndarray) – 
          Second point to represent a line.

Returns:

  • distance ( float ) –

    Calculated distance.

Source code in odak/tools/vector.py 
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def point_to_ray_distance(point, ray_point_0, ray_point_1):
    """
    Definition to find point's closest distance to a line represented with two points.

    Parameters
    ----------
    point       : ndarray
                  Point to be tested.
    ray_point_0 : ndarray
                  First point to represent a line.
    ray_point_1 : ndarray
                  Second point to represent a line.

    Returns
    ----------
    distance    : float
                  Calculated distance.
    """
    distance = np.sum(np.cross((point-ray_point_0), (point-ray_point_1))
                      ** 2)/np.sum((ray_point_1-ray_point_0)**2)
    return distance

quantize(image_field, bits=4)

Definitio to quantize a image field (0-255, 8 bit) to a certain bits level.

Parameters:

  • image_field (ndarray) – 
          Input image field.
  • bits – 
          A value in between 0 to 8. Can not be zero.

Returns:

  • new_field ( ndarray ) –

    Quantized image field.

Source code in odak/tools/matrix.py 
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def quantize(image_field, bits=4):
    """
    Definitio to quantize a image field (0-255, 8 bit) to a certain bits level.

    Parameters
    ----------
    image_field : ndarray
                  Input image field.
    bits        : int
                  A value in between 0 to 8. Can not be zero.

    Returns
    ----------
    new_field   : ndarray
                  Quantized image field.
    """
    divider = 2**(8-bits)
    new_field = image_field/divider
    new_field = new_field.astype(np.int64)
    return new_field

random_sample_point_cloud(point_cloud, no, p=None)

Definition to pull a subset of points from a point cloud with a given probability.

Parameters:

  • point_cloud – 
           Point cloud array.
  • no – 
           Number of samples.
  • p – 
           Probability list in the same size as no.

Returns:

  • subset ( ndarray ) –

    Subset of the given point cloud.

Source code in odak/tools/sample.py 
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def random_sample_point_cloud(point_cloud, no, p=None):
    """
    Definition to pull a subset of points from a point cloud with a given probability.

    Parameters
    ----------
    point_cloud  : ndarray
                   Point cloud array.
    no           : list
                   Number of samples.
    p            : list
                   Probability list in the same size as no.

    Returns
    ----------
    subset       : ndarray
                   Subset of the given point cloud.
    """
    choice = np.random.choice(point_cloud.shape[0], no, p)
    subset = point_cloud[choice, :]
    return subset

read_PLY(fn, offset=[0, 0, 0], angles=[0.0, 0.0, 0.0], mode='XYZ')

Definition to read a PLY file and extract meshes from a given PLY file. Note that rotation is always with respect to 0,0,0.

Parameters:

  • fn – 
           Filename of a PLY file.
  • offset – 
           Offset in X,Y,Z.
  • angles – 
           Rotation angles in degrees.
  • mode – 
           Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.

Returns:

  • triangles ( ndarray ) –

    Triangles from a given PLY file. Note that the triangles coming out of this function isn't always structured in the right order and with the size of (MxN)x3. You can use numpy's reshape to restructure it to mxnx3 if you know what you are doing.

Source code in odak/tools/asset.py 
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def read_PLY(fn, offset=[0, 0, 0], angles=[0., 0., 0.], mode='XYZ'):
    """
    Definition to read a PLY file and extract meshes from a given PLY file. Note that rotation is always with respect to 0,0,0.

    Parameters
    ----------
    fn           : string
                   Filename of a PLY file.
    offset       : ndarray
                   Offset in X,Y,Z.
    angles       : list
                   Rotation angles in degrees.
    mode         : str
                   Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes. 

    Returns
    ----------
    triangles    : ndarray
                  Triangles from a given PLY file. Note that the triangles coming out of this function isn't always structured in the right order and with the size of (MxN)x3. You can use numpy's reshape to restructure it to mxnx3 if you know what you are doing.
    """
    if np.__name__ != 'numpy':
        import numpy as np_ply
    else:
        np_ply = np
    with open(fn, 'rb') as f:
        plydata = PlyData.read(f)
    triangle_ids = np_ply.vstack(plydata['face'].data['vertex_indices'])
    triangles = []
    for vertex_ids in triangle_ids:
        triangle = [
            rotate_point(plydata['vertex'][int(vertex_ids[0])
                                           ].tolist(), angles=angles, offset=offset)[0],
            rotate_point(plydata['vertex'][int(vertex_ids[1])
                                           ].tolist(), angles=angles, offset=offset)[0],
            rotate_point(plydata['vertex'][int(vertex_ids[2])
                                           ].tolist(), angles=angles, offset=offset)[0]
        ]
        triangle = np_ply.asarray(triangle)
        triangles.append(triangle)
    triangles = np_ply.array(triangles)
    triangles = np.asarray(triangles, dtype=np.float32)
    return triangles

read_PLY_point_cloud(filename)

Definition to read a PLY file as a point cloud.

Parameters:

  • filename – 
           Filename of a PLY file.

Returns:

  • point_cloud ( ndarray ) –

    An array filled with poitns from the PLY file.

Source code in odak/tools/asset.py 
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def read_PLY_point_cloud(filename):
    """
    Definition to read a PLY file as a point cloud.

    Parameters
    ----------
    filename     : str
                   Filename of a PLY file.

    Returns
    ----------
    point_cloud  : ndarray
                   An array filled with poitns from the PLY file.
    """
    plydata = PlyData.read(filename)
    if np.__name__ != 'numpy':
        import numpy as np_ply
        point_cloud = np_ply.zeros((plydata['vertex'][:].shape[0], 3))
        point_cloud[:, 0] = np_ply.asarray(plydata['vertex']['x'][:])
        point_cloud[:, 1] = np_ply.asarray(plydata['vertex']['y'][:])
        point_cloud[:, 2] = np_ply.asarray(plydata['vertex']['z'][:])
        point_cloud = np.asarray(point_cloud)
    else:
        point_cloud = np.zeros((plydata['vertex'][:].shape[0], 3))
        point_cloud[:, 0] = np.asarray(plydata['vertex']['x'][:])
        point_cloud[:, 1] = np.asarray(plydata['vertex']['y'][:])
        point_cloud[:, 2] = np.asarray(plydata['vertex']['z'][:])
    return point_cloud

read_text_file(filename)

Definition to read a given text file and convert it into a Pythonic list.

Parameters:

  • filename – 
              Source filename (i.e. test.txt).

Returns:

  • content ( list ) –

    Pythonic string list containing the text from the file provided.

Source code in odak/tools/file.py 
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def read_text_file(filename):
    """
    Definition to read a given text file and convert it into a Pythonic list.


    Parameters
    ----------
    filename        : str
                      Source filename (i.e. test.txt).


    Returns
    -------
    content         : list
                      Pythonic string list containing the text from the file provided.
    """
    content = []
    loaded_file = open(expanduser(filename))
    while line := loaded_file.readline():
        content.append(line.rstrip())
    return content

resize_image(img, target_size)

Definition to resize a given image to a target shape.

Parameters:

  • img – 
            MxN image to be resized.
        Image must be normalized (0-1).
  • target_size – 
            Target shape.

Returns:

  • img ( ndarray ) –

    Resized image.

Source code in odak/tools/file.py 
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def resize_image(img, target_size):
    """
    Definition to resize a given image to a target shape.


    Parameters
    ----------
    img           : ndarray
                    MxN image to be resized.
                    Image must be normalized (0-1).
    target_size   : list
                    Target shape.


    Returns
    ----------
    img           : ndarray
                    Resized image.

    """
    img = cv2.resize(img, dsize=(target_size[0], target_size[1]), interpolation=cv2.INTER_AREA)
    return img

rotate_point(point, angles=[0, 0, 0], mode='XYZ', origin=[0, 0, 0], offset=[0, 0, 0])

Definition to rotate a given point. Note that rotation is always with respect to 0,0,0.

Parameters:

  • point – 
           A point.
  • angles – 
           Rotation angles in degrees.
  • mode – 
           Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.
  • origin – 
           Reference point for a rotation.
  • offset – 
           Shift with the given offset.

Returns:

  • result ( ndarray ) –

    Result of the rotation

  • rotx ( ndarray ) –

    Rotation matrix along X axis.

  • roty ( ndarray ) –

    Rotation matrix along Y axis.

  • rotz ( ndarray ) –

    Rotation matrix along Z axis.

Source code in odak/tools/transformation.py 
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def rotate_point(point, angles = [0, 0, 0], mode = 'XYZ', origin = [0, 0, 0], offset = [0, 0, 0]):
    """
    Definition to rotate a given point. Note that rotation is always with respect to 0,0,0.

    Parameters
    ----------
    point        : ndarray
                   A point.
    angles       : list
                   Rotation angles in degrees. 
    mode         : str
                   Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.
    origin       : list
                   Reference point for a rotation.
    offset       : list
                   Shift with the given offset.

    Returns
    ----------
    result       : ndarray
                   Result of the rotation
    rotx         : ndarray
                   Rotation matrix along X axis.
    roty         : ndarray
                   Rotation matrix along Y axis.
    rotz         : ndarray
                   Rotation matrix along Z axis.
    """
    point = np.asarray(point)
    point -= np.asarray(origin)
    rotx = rotmatx(angles[0])
    roty = rotmaty(angles[1])
    rotz = rotmatz(angles[2])
    if mode == 'XYZ':
        result = np.dot(rotz, np.dot(roty, np.dot(rotx, point)))
    elif mode == 'XZY':
        result = np.dot(roty, np.dot(rotz, np.dot(rotx, point)))
    elif mode == 'YXZ':
        result = np.dot(rotz, np.dot(rotx, np.dot(roty, point)))
    elif mode == 'ZXY':
        result = np.dot(roty, np.dot(rotx, np.dot(rotz, point)))
    elif mode == 'ZYX':
        result = np.dot(rotx, np.dot(roty, np.dot(rotz, point)))
    result += np.asarray(origin)
    result += np.asarray(offset)
    return result, rotx, roty, rotz

rotate_points(points, angles=[0, 0, 0], mode='XYZ', origin=[0, 0, 0], offset=[0, 0, 0])

Definition to rotate points.

Parameters:

  • points – 
           Points.
  • angles – 
           Rotation angles in degrees.
  • mode – 
           Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.
  • origin – 
           Reference point for a rotation.
  • offset – 
           Shift with the given offset.

Returns:

  • result ( ndarray ) –

    Result of the rotation

Source code in odak/tools/transformation.py 
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def rotate_points(points, angles = [0, 0, 0], mode = 'XYZ', origin = [0, 0, 0], offset = [0, 0, 0]):
    """
    Definition to rotate points.

    Parameters
    ----------
    points       : ndarray
                   Points.
    angles       : list
                   Rotation angles in degrees. 
    mode         : str
                   Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.
    origin       : list
                   Reference point for a rotation.
    offset       : list
                   Shift with the given offset.

    Returns
    ----------
    result       : ndarray
                   Result of the rotation   
    """
    points = np.asarray(points)
    if angles[0] == 0 and angles[1] == 0 and angles[2] == 0:
        result = np.array(offset) + points
        return result
    points -= np.array(origin)
    rotx = rotmatx(angles[0])
    roty = rotmaty(angles[1])
    rotz = rotmatz(angles[2])
    if mode == 'XYZ':
        result = np.dot(rotz, np.dot(roty, np.dot(rotx, points.T))).T
    elif mode == 'XZY':
        result = np.dot(roty, np.dot(rotz, np.dot(rotx, points.T))).T
    elif mode == 'YXZ':
        result = np.dot(rotz, np.dot(rotx, np.dot(roty, points.T))).T
    elif mode == 'ZXY':
        result = np.dot(roty, np.dot(rotx, np.dot(rotz, points.T))).T
    elif mode == 'ZYX':
        result = np.dot(rotx, np.dot(roty, np.dot(rotz, points.T))).T
    result += np.array(origin)
    result += np.array(offset)
    return result

rotmatx(angle)

Definition to generate a rotation matrix along X axis.

Parameters:

  • angle – 
           Rotation angles in degrees.

Returns:

  • rotx ( ndarray ) –

    Rotation matrix along X axis.

Source code in odak/tools/transformation.py 
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def rotmatx(angle):
    """
    Definition to generate a rotation matrix along X axis.

    Parameters
    ----------
    angle        : list
                   Rotation angles in degrees.

    Returns
    -------
    rotx         : ndarray
                   Rotation matrix along X axis.
    """
    angle = np.float64(angle)
    angle = np.radians(angle)
    rotx = np.array([
        [1.,               0.,               0.],
        [0.,  math.cos(angle), -math.sin(angle)],
        [0.,  math.sin(angle),  math.cos(angle)]
    ], dtype=np.float64)
    return rotx

rotmaty(angle)

Definition to generate a rotation matrix along Y axis.

Parameters:

  • angle – 
           Rotation angles in degrees.

Returns:

  • roty ( ndarray ) –

    Rotation matrix along Y axis.

Source code in odak/tools/transformation.py 
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def rotmaty(angle):
    """
    Definition to generate a rotation matrix along Y axis.

    Parameters
    ----------
    angle        : list
                   Rotation angles in degrees.

    Returns
    -------
    roty         : ndarray
                   Rotation matrix along Y axis.
    """
    angle = np.radians(angle)
    roty = np.array([
        [math.cos(angle),  0., math.sin(angle)],
        [0.,               1.,              0.],
        [-math.sin(angle), 0., math.cos(angle)]
    ], dtype=np.float64)
    return roty

rotmatz(angle)

Definition to generate a rotation matrix along Z axis.

Parameters:

  • angle – 
           Rotation angles in degrees.

Returns:

  • rotz ( ndarray ) –

    Rotation matrix along Z axis.

Source code in odak/tools/transformation.py 
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def rotmatz(angle):
    """
    Definition to generate a rotation matrix along Z axis.

    Parameters
    ----------
    angle        : list
                   Rotation angles in degrees.

    Returns
    -------
    rotz         : ndarray
                   Rotation matrix along Z axis.
    """
    angle = np.radians(angle)
    rotz = np.array([
        [math.cos(angle), -math.sin(angle), 0.],
        [math.sin(angle),  math.cos(angle), 0.],
        [0.,               0., 1.]
    ], dtype=np.float64)

    return rotz

same_side(p1, p2, a, b)

Definition to figure which side a point is on with respect to a line and a point. See http://www.blackpawn.com/texts/pointinpoly/ for more. If p1 and p2 are on the sameside, this definition returns True.

Parameters:

  • p1 – 
          Point(s) to check.
  • p2 – 
          This is the point check against.
  • a – 
          First point that forms the line.
  • b – 
          Second point that forms the line.
Source code in odak/tools/vector.py 
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def same_side(p1, p2, a, b):
    """
    Definition to figure which side a point is on with respect to a line and a point. See http://www.blackpawn.com/texts/pointinpoly/ for more. If p1 and p2 are on the sameside, this definition returns True.

    Parameters
    ----------
    p1          : list
                  Point(s) to check.
    p2          : list
                  This is the point check against.
    a           : list
                  First point that forms the line.
    b           : list
                  Second point that forms the line.
    """
    ba = np.subtract(b, a)
    p1a = np.subtract(p1, a)
    p2a = np.subtract(p2, a)
    cp1 = np.cross(ba, p1a)
    cp2 = np.cross(ba, p2a)
    test = np.dot(cp1, cp2)
    if len(p1.shape) > 1:
        return test >= 0
    if test >= 0:
        return True
    return False

save_dictionary(settings, filename)

Definition to load a dictionary (JSON) file.

Parameters:

  • settings – 
            Dictionary read from the file.
  • filename – 
            Filename.
Source code in odak/tools/file.py 
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def save_dictionary(settings, filename):
    """
    Definition to load a dictionary (JSON) file.


    Parameters
    ----------
    settings      : dict
                    Dictionary read from the file.
    filename      : str
                    Filename.
    """
    with open(expanduser(filename), 'w', encoding='utf-8') as f:
        json.dump(settings, f, ensure_ascii=False, indent=4)
    return settings

save_image(fn, img, cmin=0, cmax=255, color_depth=8)

Definition to save a Numpy array as an image.

Parameters:

  • fn – 
           Filename.
  • img – 
           A numpy array with NxMx3 or NxMx1 shapes.
  • cmin – 
           Minimum value that will be interpreted as 0 level in the final image.
  • cmax – 
           Maximum value that will be interpreted as 255 level in the final image.
  • color_depth – 
           Pixel color depth in bits, default is eight bits.

Returns:

  • bool ( bool ) –

    True if successful.

Source code in odak/tools/file.py 
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def save_image(fn, img, cmin = 0, cmax = 255, color_depth = 8):
    """
    Definition to save a Numpy array as an image.


    Parameters
    ----------
    fn           : str
                   Filename.
    img          : ndarray
                   A numpy array with NxMx3 or NxMx1 shapes.
    cmin         : int
                   Minimum value that will be interpreted as 0 level in the final image.
    cmax         : int
                   Maximum value that will be interpreted as 255 level in the final image.
    color_depth  : int
                   Pixel color depth in bits, default is eight bits.


    Returns
    ----------
    bool         :  bool
                    True if successful.

    """
    input_img = np.copy(img).astype(np.float32)
    cmin = float(cmin)
    cmax = float(cmax)
    input_img[input_img < cmin] = cmin
    input_img[input_img > cmax] = cmax
    input_img /= cmax
    input_img = input_img * 1. * (2**color_depth - 1)
    if color_depth == 8:
        input_img = input_img.astype(np.uint8)
    elif color_depth == 16:
        input_img = input_img.astype(np.uint16)
    if len(input_img.shape) > 2:
        if input_img.shape[2] > 1:
            cache_img = np.copy(input_img)
            cache_img[:, :, 0] = input_img[:, :, 2]
            cache_img[:, :, 2] = input_img[:, :, 0]
            input_img = cache_img
    cv2.imwrite(expanduser(fn), input_img)
    return True

shell_command(cmd, cwd='.', timeout=None, check=True)

Definition to initiate shell commands.

Parameters:

  • cmd – 
           Command to be executed.
  • cwd – 
           Working directory.
  • timeout – 
           Timeout if the process isn't complete in the given number of seconds.
  • check – 
           Set it to True to return the results and to enable timeout.

Returns:

  • proc ( Popen ) –

    Generated process.

  • outs ( str ) –

    Outputs of the executed command, returns None when check is set to False.

  • errs ( str ) –

    Errors of the executed command, returns None when check is set to False.

Source code in odak/tools/file.py 
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def shell_command(cmd, cwd = '.', timeout = None, check = True):
    """
    Definition to initiate shell commands.


    Parameters
    ----------
    cmd          : list
                   Command to be executed. 
    cwd          : str
                   Working directory.
    timeout      : int
                   Timeout if the process isn't complete in the given number of seconds.
    check        : bool
                   Set it to True to return the results and to enable timeout.


    Returns
    ----------
    proc         : subprocess.Popen
                   Generated process.
    outs         : str
                   Outputs of the executed command, returns None when check is set to False.
    errs         : str
                   Errors of the executed command, returns None when check is set to False.

    """
    for item_id in range(len(cmd)):
        cmd[item_id] = expanduser(cmd[item_id])
    proc = subprocess.Popen(
                            cmd,
                            cwd = cwd,
                            stdout = subprocess.PIPE
                           )
    if check == False:
        return proc, None, None
    try:
        outs, errs = proc.communicate(timeout = timeout)
    except subprocess.TimeoutExpired:
        proc.kill()
        outs, errs = proc.communicate()
    return proc, outs, errs

size_of_a_file(file_path)

A definition to get size of a file with a relevant unit.

Parameters:

  • file_path – 
         Path of the file.

Returns:

  • a ( float ) –

    Size of the file.

  • b ( str ) –

    Unit of the size (bytes, KB, MB, GB or TB).

Source code in odak/tools/file.py 
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def size_of_a_file(file_path):
    """
    A definition to get size of a file with a relevant unit.


    Parameters
    ----------
    file_path  : float
                 Path of the file.


    Returns
    ----------
    a          : float
                 Size of the file.
    b          : str
                 Unit of the size (bytes, KB, MB, GB or TB).
    """
    if os.path.isfile(file_path):
        file_info = os.stat(file_path)
        a, b = convert_bytes(file_info.st_size)
        return a, b
    return None, None

sphere_sample(no=[10, 10], radius=1.0, center=[0.0, 0.0, 0.0], k=[1, 2])

Definition to generate a regular sample set on the surface of a sphere using polar coordinates.

Parameters:

  • no – 
          Number of samples.
  • radius – 
          Radius of a sphere.
  • center – 
          Center of a sphere.
  • k – 
          Multipliers for gathering samples. If you set k=[1,2] it will draw samples from a perfect sphere.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def sphere_sample(no=[10, 10], radius=1., center=[0., 0., 0.], k=[1, 2]):
    """
    Definition to generate a regular sample set on the surface of a sphere using polar coordinates.

    Parameters
    ----------
    no          : list
                  Number of samples.
    radius      : float
                  Radius of a sphere.
    center      : list
                  Center of a sphere.
    k           : list
                  Multipliers for gathering samples. If you set k=[1,2] it will draw samples from a perfect sphere.

    Returns
    ----------
    samples     : ndarray
                  Samples generated.
    """
    samples = np.zeros((no[0], no[1], 3))
    psi, teta = np.mgrid[0:no[0], 0:no[1]]
    psi = k[0]*np.pi/no[0]*psi
    teta = k[1]*np.pi/no[1]*teta
    samples[:, :, 0] = center[0]+radius*np.sin(psi)*np.cos(teta)
    samples[:, :, 1] = center[0]+radius*np.sin(psi)*np.sin(teta)
    samples[:, :, 2] = center[0]+radius*np.cos(psi)
    samples = samples.reshape((no[0]*no[1], 3))
    return samples

sphere_sample_uniform(no=[10, 10], radius=1.0, center=[0.0, 0.0, 0.0], k=[1, 2])

Definition to generate an uniform sample set on the surface of a sphere using polar coordinates.

Parameters:

  • no – 
          Number of samples.
  • radius – 
          Radius of a sphere.
  • center – 
          Center of a sphere.
  • k – 
          Multipliers for gathering samples. If you set k=[1,2] it will draw samples from a perfect sphere.

Returns:

  • samples ( ndarray ) –

    Samples generated.

Source code in odak/tools/sample.py 
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def sphere_sample_uniform(no=[10, 10], radius=1., center=[0., 0., 0.], k=[1, 2]):
    """
    Definition to generate an uniform sample set on the surface of a sphere using polar coordinates.

    Parameters
    ----------
    no          : list
                  Number of samples.
    radius      : float
                  Radius of a sphere.
    center      : list
                  Center of a sphere.
    k           : list
                  Multipliers for gathering samples. If you set k=[1,2] it will draw samples from a perfect sphere.


    Returns
    ----------
    samples     : ndarray
                  Samples generated.

    """
    samples = np.zeros((no[0], no[1], 3))
    row = np.arange(0, no[0])
    psi, teta = np.mgrid[0:no[0], 0:no[1]]
    for psi_id in range(0, no[0]):
        psi[psi_id] = np.roll(row, psi_id, axis=0)
        teta[psi_id] = np.roll(row, -psi_id, axis=0)
    psi = k[0]*np.pi/no[0]*psi
    teta = k[1]*np.pi/no[1]*teta
    samples[:, :, 0] = center[0]+radius*np.sin(psi)*np.cos(teta)
    samples[:, :, 1] = center[1]+radius*np.sin(psi)*np.sin(teta)
    samples[:, :, 2] = center[2]+radius*np.cos(psi)
    samples = samples.reshape((no[0]*no[1], 3))
    return samples

tilt_towards(location, lookat)

Definition to tilt surface normal of a plane towards a point.

Parameters:

  • location – 
           Center of the plane to be tilted.
  • lookat – 
           Tilt towards this point.

Returns:

  • angles ( list ) –

    Rotation angles in degrees.

Source code in odak/tools/transformation.py 
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def tilt_towards(location, lookat):
    """
    Definition to tilt surface normal of a plane towards a point.

    Parameters
    ----------
    location     : list
                   Center of the plane to be tilted.
    lookat       : list
                   Tilt towards this point.

    Returns
    ----------
    angles       : list
                   Rotation angles in degrees.
    """
    dx = location[0]-lookat[0]
    dy = location[1]-lookat[1]
    dz = location[2]-lookat[2]
    dist = np.sqrt(dx**2+dy**2+dz**2)
    phi = np.arctan2(dy, dx)
    theta = np.arccos(dz/dist)
    angles = [
        0,
        np.degrees(theta).tolist(),
        np.degrees(phi).tolist()
    ]
    return angles

write_PLY(triangles, savefn='output.ply')

Definition to generate a PLY file from given points.

Parameters:

  • triangles – 
          List of triangles with the size of Mx3x3.
  • savefn – 
          Filename for a PLY file.
Source code in odak/tools/asset.py 
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def write_PLY(triangles, savefn = 'output.ply'):
    """
    Definition to generate a PLY file from given points.

    Parameters
    ----------
    triangles   : ndarray
                  List of triangles with the size of Mx3x3.
    savefn      : string
                  Filename for a PLY file.
    """
    tris = []
    pnts = []
    color = [255, 255, 255]
    for tri_id in range(triangles.shape[0]):
        tris.append(
            (
                [3*tri_id, 3*tri_id+1, 3*tri_id+2],
                color[0],
                color[1],
                color[2]
            )
        )
        for i in range(0, 3):
            pnts.append(
                (
                    float(triangles[tri_id][i][0]),
                    float(triangles[tri_id][i][1]),
                    float(triangles[tri_id][i][2])
                )
            )
    tris = np.asarray(tris, dtype=[
                          ('vertex_indices', 'i4', (3,)), ('red', 'u1'), ('green', 'u1'), ('blue', 'u1')])
    pnts = np.asarray(pnts, dtype=[('x', 'f4'), ('y', 'f4'), ('z', 'f4')])
    # Save mesh.
    el1 = PlyElement.describe(pnts, 'vertex', comments=['Vertex data'])
    el2 = PlyElement.describe(tris, 'face', comments=['Face data'])
    PlyData([el1, el2], text="True").write(savefn)

write_PLY_from_points(points, savefn='output.ply')

Definition to generate a PLY file from given points.

Parameters:

  • points – 
          List of points with the size of MxNx3.
  • savefn – 
          Filename for a PLY file.
Source code in odak/tools/asset.py 
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def write_PLY_from_points(points, savefn='output.ply'):
    """
    Definition to generate a PLY file from given points.

    Parameters
    ----------
    points      : ndarray
                  List of points with the size of MxNx3.
    savefn      : string
                  Filename for a PLY file.

    """
    if np.__name__ != 'numpy':
        import numpy as np_ply
    else:
        np_ply = np
    # Generate equation
    samples = [points.shape[0], points.shape[1]]
    # Generate vertices.
    pnts = []
    tris = []
    for idx in range(0, samples[0]):
        for idy in range(0, samples[1]):
            pnt = (points[idx, idy, 0],
                   points[idx, idy, 1], points[idx, idy, 2])
            pnts.append(pnt)
    color = [255, 255, 255]
    for idx in range(0, samples[0]-1):
        for idy in range(0, samples[1]-1):
            tris.append(([idy+(idx+1)*samples[0], idy+idx*samples[0],
                        idy+1+idx*samples[0]], color[0], color[1], color[2]))
            tris.append(([idy+(idx+1)*samples[0], idy+1+idx*samples[0],
                        idy+1+(idx+1)*samples[0]], color[0], color[1], color[2]))
    tris = np_ply.asarray(tris, dtype=[(
        'vertex_indices', 'i4', (3,)), ('red', 'u1'), ('green', 'u1'), ('blue', 'u1')])
    pnts = np_ply.asarray(pnts, dtype=[('x', 'f4'), ('y', 'f4'), ('z', 'f4')])
    # Save mesh.
    el1 = PlyElement.describe(pnts, 'vertex', comments=['Vertex data'])
    el2 = PlyElement.describe(tris, 'face', comments=['Face data'])
    PlyData([el1, el2], text="True").write(savefn)

write_to_text_file(content, filename, write_flag='w')

Defininition to write a Pythonic list to a text file.

Parameters:

  • content – 
              Pythonic string list to be written to a file.
  • filename – 
              Destination filename (i.e. test.txt).
  • write_flag – 
              Defines the interaction with the file. 
          The default is "w" (overwrite any existing content).
          For more see: https://docs.python.org/3/tutorial/inputoutput.html#reading-and-writing-files
Source code in odak/tools/file.py 
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def write_to_text_file(content, filename, write_flag = 'w'):
    """
    Defininition to write a Pythonic list to a text file.


    Parameters
    ----------
    content         : list
                      Pythonic string list to be written to a file.
    filename        : str
                      Destination filename (i.e. test.txt).
    write_flag      : str
                      Defines the interaction with the file. 
                      The default is "w" (overwrite any existing content).
                      For more see: https://docs.python.org/3/tutorial/inputoutput.html#reading-and-writing-files
    """
    with open(expanduser(filename), write_flag) as f:
        for line in content:
            f.write('{}\n'.format(line))
    return True

zero_pad(field, size=None, method='center')

Definition to zero pad a MxN array to 2Mx2N array.

Parameters:

  • field – 
                Input field MxN array.
  • size – 
                Size to be zeropadded.
  • method – 
                Zeropad either by placing the content to center or to the left.

Returns:

  • field_zero_padded ( ndarray ) –

    Zeropadded version of the input field.

Source code in odak/tools/matrix.py 
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def zero_pad(field, size=None, method='center'):
    """
    Definition to zero pad a MxN array to 2Mx2N array.

    Parameters
    ----------
    field             : ndarray
                        Input field MxN array.
    size              : list
                        Size to be zeropadded.
    method            : str
                        Zeropad either by placing the content to center or to the left.

    Returns
    ----------
    field_zero_padded : ndarray
                        Zeropadded version of the input field.
    """
    if type(size) == type(None):
        hx = int(np.ceil(field.shape[0])/2)
        hy = int(np.ceil(field.shape[1])/2)
    else:
        hx = int(np.ceil((size[0]-field.shape[0])/2))
        hy = int(np.ceil((size[1]-field.shape[1])/2))
    if method == 'center':
        field_zero_padded = np.pad(
            field, ([hx, hx], [hy, hy]), constant_values=(0, 0))
    elif method == 'left aligned':
        field_zero_padded = np.pad(
            field, ([0, 2*hx], [0, 2*hy]), constant_values=(0, 0))
    if type(size) != type(None):
        field_zero_padded = field_zero_padded[0:size[0], 0:size[1]]
    return field_zero_padded

read_PLY(fn, offset=[0, 0, 0], angles=[0.0, 0.0, 0.0], mode='XYZ')

Definition to read a PLY file and extract meshes from a given PLY file. Note that rotation is always with respect to 0,0,0.

Parameters:

  • fn – 
           Filename of a PLY file.
  • offset – 
           Offset in X,Y,Z.
  • angles – 
           Rotation angles in degrees.
  • mode – 
           Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes.

Returns:

  • triangles ( ndarray ) –

    Triangles from a given PLY file. Note that the triangles coming out of this function isn't always structured in the right order and with the size of (MxN)x3. You can use numpy's reshape to restructure it to mxnx3 if you know what you are doing.

Source code in odak/tools/asset.py 
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def read_PLY(fn, offset=[0, 0, 0], angles=[0., 0., 0.], mode='XYZ'):
    """
    Definition to read a PLY file and extract meshes from a given PLY file. Note that rotation is always with respect to 0,0,0.

    Parameters
    ----------
    fn           : string
                   Filename of a PLY file.
    offset       : ndarray
                   Offset in X,Y,Z.
    angles       : list
                   Rotation angles in degrees.
    mode         : str
                   Rotation mode determines ordering of the rotations at each axis. There are XYZ,YXZ,ZXY and ZYX modes. 

    Returns
    ----------
    triangles    : ndarray
                  Triangles from a given PLY file. Note that the triangles coming out of this function isn't always structured in the right order and with the size of (MxN)x3. You can use numpy's reshape to restructure it to mxnx3 if you know what you are doing.
    """
    if np.__name__ != 'numpy':
        import numpy as np_ply
    else:
        np_ply = np
    with open(fn, 'rb') as f:
        plydata = PlyData.read(f)
    triangle_ids = np_ply.vstack(plydata['face'].data['vertex_indices'])
    triangles = []
    for vertex_ids in triangle_ids:
        triangle = [
            rotate_point(plydata['vertex'][int(vertex_ids[0])
                                           ].tolist(), angles=angles, offset=offset)[0],
            rotate_point(plydata['vertex'][int(vertex_ids[1])
                                           ].tolist(), angles=angles, offset=offset)[0],
            rotate_point(plydata['vertex'][int(vertex_ids[2])
                                           ].tolist(), angles=angles, offset=offset)[0]
        ]
        triangle = np_ply.asarray(triangle)
        triangles.append(triangle)
    triangles = np_ply.array(triangles)
    triangles = np.asarray(triangles, dtype=np.float32)
    return triangles

read_PLY_point_cloud(filename)

Definition to read a PLY file as a point cloud.

Parameters:

  • filename – 
           Filename of a PLY file.

Returns:

  • point_cloud ( ndarray ) –

    An array filled with poitns from the PLY file.

Source code in odak/tools/asset.py 
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def read_PLY_point_cloud(filename):
    """
    Definition to read a PLY file as a point cloud.

    Parameters
    ----------
    filename     : str
                   Filename of a PLY file.

    Returns
    ----------
    point_cloud  : ndarray
                   An array filled with poitns from the PLY file.
    """
    plydata = PlyData.read(filename)
    if np.__name__ != 'numpy':
        import numpy as np_ply
        point_cloud = np_ply.zeros((plydata['vertex'][:].shape[0], 3))
        point_cloud[:, 0] = np_ply.asarray(plydata['vertex']['x'][:])
        point_cloud[:, 1] = np_ply.asarray(plydata['vertex']['y'][:])
        point_cloud[:, 2] = np_ply.asarray(plydata['vertex']['z'][:])
        point_cloud = np.asarray(point_cloud)
    else:
        point_cloud = np.zeros((plydata['vertex'][:].shape[0], 3))
        point_cloud[:, 0] = np.asarray(plydata['vertex']['x'][:])
        point_cloud[:, 1] = np.asarray(plydata['vertex']['y'][:])
        point_cloud[:, 2] = np.asarray(plydata['vertex']['z'][:])
    return point_cloud

write_PLY(triangles, savefn='output.ply')

Definition to generate a PLY file from given points.

Parameters:

  • triangles – 
          List of triangles with the size of Mx3x3.
  • savefn – 
          Filename for a PLY file.
Source code in odak/tools/asset.py 
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def write_PLY(triangles, savefn = 'output.ply'):
    """
    Definition to generate a PLY file from given points.

    Parameters
    ----------
    triangles   : ndarray
                  List of triangles with the size of Mx3x3.
    savefn      : string
                  Filename for a PLY file.
    """
    tris = []
    pnts = []
    color = [255, 255, 255]
    for tri_id in range(triangles.shape[0]):
        tris.append(
            (
                [3*tri_id, 3*tri_id+1, 3*tri_id+2],
                color[0],
                color[1],
                color[2]
            )
        )
        for i in range(0, 3):
            pnts.append(
                (
                    float(triangles[tri_id][i][0]),
                    float(triangles[tri_id][i][1]),
                    float(triangles[tri_id][i][2])
                )
            )
    tris = np.asarray(tris, dtype=[
                          ('vertex_indices', 'i4', (3,)), ('red', 'u1'), ('green', 'u1'), ('blue', 'u1')])
    pnts = np.asarray(pnts, dtype=[('x', 'f4'), ('y', 'f4'), ('z', 'f4')])
    # Save mesh.
    el1 = PlyElement.describe(pnts, 'vertex', comments=['Vertex data'])
    el2 = PlyElement.describe(tris, 'face', comments=['Face data'])
    PlyData([el1, el2], text="True").write(savefn)

write_PLY_from_points(points, savefn='output.ply')

Definition to generate a PLY file from given points.

Parameters:

  • points – 
          List of points with the size of MxNx3.
  • savefn – 
          Filename for a PLY file.
Source code in odak/tools/asset.py 
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def write_PLY_from_points(points, savefn='output.ply'):
    """
    Definition to generate a PLY file from given points.

    Parameters
    ----------
    points      : ndarray
                  List of points with the size of MxNx3.
    savefn      : string
                  Filename for a PLY file.

    """
    if np.__name__ != 'numpy':
        import numpy as np_ply
    else:
        np_ply = np
    # Generate equation
    samples = [points.shape[0], points.shape[1]]
    # Generate vertices.
    pnts = []
    tris = []
    for idx in range(0, samples[0]):
        for idy in range(0, samples[1]):
            pnt = (points[idx, idy, 0],
                   points[idx, idy, 1], points[idx, idy, 2])
            pnts.append(pnt)
    color = [255, 255, 255]
    for idx in range(0, samples[0]-1):
        for idy in range(0, samples[1]-1):
            tris.append(([idy+(idx+1)*samples[0], idy+idx*samples[0],
                        idy+1+idx*samples[0]], color[0], color[1], color[2]))
            tris.append(([idy+(idx+1)*samples[0], idy+1+idx*samples[0],
                        idy+1+(idx+1)*samples[0]], color[0], color[1], color[2]))
    tris = np_ply.asarray(tris, dtype=[(
        'vertex_indices', 'i4', (3,)), ('red', 'u1'), ('green', 'u1'), ('blue', 'u1')])
    pnts = np_ply.asarray(pnts, dtype=[('x', 'f4'), ('y', 'f4'), ('z', 'f4')])
    # Save mesh.
    el1 = PlyElement.describe(pnts, 'vertex', comments=['Vertex data'])
    el2 = PlyElement.describe(tris, 'face', comments=['Face data'])
    PlyData([el1, el2], text="True").write(savefn)

convert_to_numpy(a)

A definition to convert Torch to Numpy.

Parameters:

  • a – 
         Input Torch array.

Returns:

  • b ( ndarray ) –

    Converted array.

Source code in odak/tools/conversions.py 
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def convert_to_numpy(a):
    """
    A definition to convert Torch to Numpy.

    Parameters
    ----------
    a          : torch.Tensor
                 Input Torch array.

    Returns
    ----------
    b          : numpy.ndarray
                 Converted array.
    """
    b = a.to('cpu').detach().numpy()
    return b

convert_to_torch(a, grad=True)

A definition to convert Numpy arrays to Torch.

Parameters:

  • a – 
         Input Numpy array.
  • grad – 
         Set if the converted array requires gradient.

Returns:

  • c ( Tensor ) –

    Converted array.

Source code in odak/tools/conversions.py 
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def convert_to_torch(a, grad=True):
    """
    A definition to convert Numpy arrays to Torch.

    Parameters
    ----------
    a          : ndarray
                 Input Numpy array.
    grad       : bool
                 Set if the converted array requires gradient.

    Returns
    ----------
    c          : torch.Tensor
                 Converted array.
    """
    b = np.copy(a)
    c = torch.from_numpy(b)
    c.requires_grad_(grad)
    return c

check_directory(directory)

Definition to check if a directory exist. If it doesn't exist, this definition will create one.

Parameters:

  • directory – 
            Full directory path.
Source code in odak/tools/file.py 
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def check_directory(directory):
    """
    Definition to check if a directory exist. If it doesn't exist, this definition will create one.


    Parameters
    ----------
    directory     : str
                    Full directory path.
    """
    if not os.path.exists(expanduser(directory)):
        os.makedirs(expanduser(directory))
        return False
    return True

convert_bytes(num)

A definition to convert bytes to semantic scheme (MB,GB or alike). Inspired from https://stackoverflow.com/questions/2104080/how-can-i-check-file-size-in-python#2104083.

Parameters:

  • num – 
         Size in bytes

Returns:

  • num ( float ) –

    Size in new unit.

  • x ( str ) –

    New unit bytes, KB, MB, GB or TB.

Source code in odak/tools/file.py 
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def convert_bytes(num):
    """
    A definition to convert bytes to semantic scheme (MB,GB or alike). Inspired from https://stackoverflow.com/questions/2104080/how-can-i-check-file-size-in-python#2104083.


    Parameters
    ----------
    num        : float
                 Size in bytes


    Returns
    ----------
    num        : float
                 Size in new unit.
    x          : str
                 New unit bytes, KB, MB, GB or TB.
    """
    for x in ['bytes', 'KB', 'MB', 'GB', 'TB']:
        if num < 1024.0:
            return num, x
        num /= 1024.0
    return None, None

copy_file(source, destination, follow_symlinks=True)

Definition to copy a file from one location to another.

Parameters:

  • source – 
              Source filename.
  • destination – 
              Destination filename.
  • follow_symlinks (bool, default: True ) – 
              Set to True to follow the source of symbolic links.
Source code in odak/tools/file.py 
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def copy_file(source, destination, follow_symlinks = True):
    """
    Definition to copy a file from one location to another.



    Parameters
    ----------
    source          : str
                      Source filename.
    destination     : str
                      Destination filename.
    follow_symlinks : bool
                      Set to True to follow the source of symbolic links.
    """
    return shutil.copyfile(
                           expanduser(source),
                           expanduser(source),
                           follow_symlinks = follow_symlinks
                          )

expanduser(filename)

Definition to decode filename using namespaces and shortcuts.

Parameters:

  • filename – 
            Filename.

Returns:

  • new_filename ( str ) –

    Filename.

Source code in odak/tools/file.py 
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def expanduser(filename):
    """
    Definition to decode filename using namespaces and shortcuts.


    Parameters
    ----------
    filename      : str
                    Filename.


    Returns
    -------
    new_filename  : str
                    Filename.
    """
    new_filename = os.path.expanduser(filename)
    return new_filename

list_files(path, key='*.*', recursive=True)

Definition to list files in a given path with a given key.

Parameters:

  • path – 
          Path to a folder.
  • key – 
          Key used for scanning a path.
  • recursive – 
          If set True, scan the path recursively.

Returns:

  • files_list ( ndarray ) –

    list of files found in a given path.

Source code in odak/tools/file.py 
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def list_files(path, key = '*.*', recursive = True):
    """
    Definition to list files in a given path with a given key.


    Parameters
    ----------
    path        : str
                  Path to a folder.
    key         : str
                  Key used for scanning a path.
    recursive   : bool
                  If set True, scan the path recursively.


    Returns
    ----------
    files_list  : ndarray
                  list of files found in a given path.
    """
    if recursive == True:
        search_result = pathlib.Path(expanduser(path)).rglob(key)
    elif recursive == False:
        search_result = pathlib.Path(expanduser(path)).glob(key)
    files_list = []
    for item in search_result:
        files_list.append(str(item))
    files_list = sorted(files_list)
    return files_list

load_dictionary(filename)

Definition to load a dictionary (JSON) file.

Parameters:

  • filename – 
            Filename.

Returns:

  • settings ( dict ) –

    Dictionary read from the file.

Source code in odak/tools/file.py 
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def load_dictionary(filename):
    """
    Definition to load a dictionary (JSON) file.


    Parameters
    ----------
    filename      : str
                    Filename.


    Returns
    ----------
    settings      : dict
                    Dictionary read from the file.

    """
    settings = json.load(open(expanduser(filename)))
    return settings

load_image(fn, normalizeby=0.0, torch_style=False)

Definition to load an image from a given location as a Numpy array.

Parameters:

  • fn – 
           Filename.
  • normalizeby – 
           Value to to normalize images with. Default value of zero will lead to no normalization.
  • torch_style – 
           If set True, it will load an image mxnx3 as 3xmxn.

Returns:

  • image ( ndarray ) –

    Image loaded as a Numpy array.

Source code in odak/tools/file.py 
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def load_image(fn, normalizeby = 0., torch_style = False):
    """ 
    Definition to load an image from a given location as a Numpy array.


    Parameters
    ----------
    fn           : str
                   Filename.
    normalizeby  : float
                   Value to to normalize images with. Default value of zero will lead to no normalization.
    torch_style  : bool
                   If set True, it will load an image mxnx3 as 3xmxn.


    Returns
    ----------
    image        :  ndarray
                    Image loaded as a Numpy array.

    """
    image = cv2.imread(expanduser(fn), cv2.IMREAD_UNCHANGED)
    if isinstance(image, type(None)):
         logging.warning('Image not properly loaded. Check filename or image type.')    
         sys.exit()
    if len(image.shape) > 2:
        new_image = np.copy(image)
        new_image[:, :, 0] = image[:, :, 2]
        new_image[:, :, 2] = image[:, :, 0]
        image = new_image
    if normalizeby != 0.:
        image = image * 1. / normalizeby
    if torch_style == True and len(image.shape) > 2:
        image = np.moveaxis(image, -1, 0)
    return image.astype(float)

read_text_file(filename)

Definition to read a given text file and convert it into a Pythonic list.

Parameters:

  • filename – 
              Source filename (i.e. test.txt).

Returns:

  • content ( list ) –

    Pythonic string list containing the text from the file provided.

Source code in odak/tools/file.py 
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def read_text_file(filename):
    """
    Definition to read a given text file and convert it into a Pythonic list.


    Parameters
    ----------
    filename        : str
                      Source filename (i.e. test.txt).


    Returns
    -------
    content         : list
                      Pythonic string list containing the text from the file provided.
    """
    content = []
    loaded_file = open(expanduser(filename))
    while line := loaded_file.readline():
        content.append(line.rstrip())
    return content

resize_image(img, target_size)

Definition to resize a given image to a target shape.

Parameters:

  • img – 
            MxN image to be resized.
        Image must be normalized (0-1).
  • target_size – 
            Target shape.

Returns:

  • img ( ndarray ) –

    Resized image.

Source code in odak/tools/file.py 
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def resize_image(img, target_size):
    """
    Definition to resize a given image to a target shape.


    Parameters
    ----------
    img           : ndarray
                    MxN image to be resized.
                    Image must be normalized (0-1).
    target_size   : list
                    Target shape.


    Returns
    ----------
    img           : ndarray
                    Resized image.

    """
    img = cv2.resize(img, dsize=(target_size[0], target_size[1]), interpolation=cv2.INTER_AREA)
    return img

save_dictionary(settings, filename)

Definition to load a dictionary (JSON) file.

Parameters:

  • settings – 
            Dictionary read from the file.
  • filename – 
            Filename.
Source code in odak/tools/file.py 
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def save_dictionary(settings, filename):
    """
    Definition to load a dictionary (JSON) file.


    Parameters
    ----------
    settings      : dict
                    Dictionary read from the file.
    filename      : str
                    Filename.
    """
    with open(expanduser(filename), 'w', encoding='utf-8') as f:
        json.dump(settings, f, ensure_ascii=False, indent=4)
    return settings

save_image(fn, img, cmin=0, cmax=255, color_depth=8)

Definition to save a Numpy array as an image.

Parameters:

  • fn – 
           Filename.
  • img – 
           A numpy array with NxMx3 or NxMx1 shapes.
  • cmin – 
           Minimum value that will be interpreted as 0 level in the final image.
  • cmax – 
           Maximum value that will be interpreted as 255 level in the final image.
  • color_depth – 
           Pixel color depth in bits, default is eight bits.

Returns:

  • bool ( bool ) –

    True if successful.

Source code in odak/tools/file.py 
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def save_image(fn, img, cmin = 0, cmax = 255, color_depth = 8):
    """
    Definition to save a Numpy array as an image.


    Parameters
    ----------
    fn           : str
                   Filename.
    img          : ndarray
                   A numpy array with NxMx3 or NxMx1 shapes.
    cmin         : int
                   Minimum value that will be interpreted as 0 level in the final image.
    cmax         : int
                   Maximum value that will be interpreted as 255 level in the final image.
    color_depth  : int
                   Pixel color depth in bits, default is eight bits.


    Returns
    ----------
    bool         :  bool
                    True if successful.

    """
    input_img = np.copy(img).astype(np.float32)
    cmin = float(cmin)
    cmax = float(cmax)
    input_img[input_img < cmin] = cmin
    input_img[input_img > cmax] = cmax
    input_img /= cmax
    input_img = input_img * 1. * (2**color_depth - 1)
    if color_depth == 8:
        input_img = input_img.astype(np.uint8)
    elif color_depth == 16:
        input_img = input_img.astype(np.uint16)
    if len(input_img.shape) > 2:
        if input_img.shape[2] > 1:
            cache_img = np.copy(input_img)
            cache_img[:, :, 0] = input_img[:, :, 2]
            cache_img[:, :, 2] = input_img[:, :, 0]
            input_img = cache_img
    cv2.imwrite(expanduser(fn), input_img)
    return True

shell_command(cmd, cwd='.', timeout=None, check=True)

Definition to initiate shell commands.

Parameters:

  • cmd – 
           Command to be executed.
  • cwd – 
           Working directory.
  • timeout – 
           Timeout if the process isn't complete in the given number of seconds.
  • check – 
           Set it to True to return the results and to enable timeout.

Returns:

  • proc ( Popen ) –

    Generated process.

  • outs ( str ) –

    Outputs of the executed command, returns None when check is set to False.

  • errs ( str ) –

    Errors of the executed command, returns None when check is set to False.

Source code in odak/tools/file.py 
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def shell_command(cmd, cwd = '.', timeout = None, check = True):
    """
    Definition to initiate shell commands.


    Parameters
    ----------
    cmd          : list
                   Command to be executed. 
    cwd          : str
                   Working directory.
    timeout      : int
                   Timeout if the process isn't complete in the given number of seconds.
    check        : bool
                   Set it to True to return the results and to enable timeout.


    Returns
    ----------
    proc         : subprocess.Popen
                   Generated process.
    outs         : str
                   Outputs of the executed command, returns None when check is set to False.
    errs         : str
                   Errors of the executed command, returns None when check is set to False.

    """
    for item_id in range(len(cmd)):
        cmd[item_id] = expanduser(cmd[item_id])
    proc = subprocess.Popen(
                            cmd,
                            cwd = cwd,
                            stdout = subprocess.PIPE
                           )
    if check == False:
        return proc, None, None
    try:
        outs, errs = proc.communicate(timeout = timeout)
    except subprocess.TimeoutExpired:
        proc.kill()
        outs, errs = proc.communicate()
    return proc, outs, errs

size_of_a_file(file_path)

A definition to get size of a file with a relevant unit.

Parameters:

  • file_path – 
         Path of the file.

Returns:

  • a ( float ) –

    Size of the file.

  • b ( str ) –

    Unit of the size (bytes, KB, MB, GB or TB).

Source code in odak/tools/file.py 
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def size_of_a_file(file_path):
    """
    A definition to get size of a file with a relevant unit.


    Parameters
    ----------
    file_path  : float
                 Path of the file.


    Returns
    ----------
    a          : float
                 Size of the file.
    b          : str
                 Unit of the size (bytes, KB, MB, GB or TB).
    """
    if os.path.isfile(file_path):
        file_info = os.stat(file_path)
        a, b = convert_bytes(file_info.st_size)
        return a, b
    return None, None

write_to_text_file(content, filename, write_flag='w')

Defininition to write a Pythonic list to a text file.

Parameters:

  • content – 
              Pythonic string list to be written to a file.
  • filename – 
              Destination filename (i.e. test.txt).
  • write_flag – 
              Defines the interaction with the file. 
          The default is "w" (overwrite any existing content).
          For more see: https://docs.python.org/3/tutorial/inputoutput.html#reading-and-writing-files
Source code in odak/tools/file.py 
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def write_to_text_file(content, filename, write_flag = 'w'):
    """
    Defininition to write a Pythonic list to a text file.


    Parameters
    ----------
    content         : list
                      Pythonic string list to be written to a file.
    filename        : str
                      Destination filename (i.e. test.txt).
    write_flag      : str
                      Defines the interaction with the file. 
                      The default is "w" (overwrite any existing content).
                      For more see: https://docs.python.org/3/tutorial/inputoutput.html#reading-and-writing-files
    """
    with open(expanduser(filename), write_flag) as f:
        for line in content:
            f.write('{}\n'.format(line))
    return True

A class to work with latex documents.

Source code in odak/tools/latex.py 
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class latex():
    """
    A class to work with latex documents.
    """
    def __init__(
                 self,
                 filename
                ):
        """
        Parameters
        ----------
        filename     : str
                       Source filename (i.e. sample.tex).
        """
        self.filename = filename
        self.content = read_text_file(self.filename)
        self.content_type = []
        self.latex_dictionary = [
                                 '\\documentclass',
                                 '\\if',
                                 '\\pdf',
                                 '\\else',
                                 '\\fi',
                                 '\\vgtc',
                                 '\\teaser',
                                 '\\abstract',
                                 '\\CCS',
                                 '\\usepackage',
                                 '\\PassOptionsToPackage',
                                 '\\definecolor',
                                 '\\AtBeginDocument',
                                 '\\providecommand',
                                 '\\setcopyright',
                                 '\\copyrightyear',
                                 '\\acmYear',
                                 '\\citestyle',
                                 '\\newcommand',
                                 '\\acmDOI',
                                 '\\newabbreviation',
                                 '\\global',
                                 '\\begin{document}',
                                 '\\author',
                                 '\\affiliation',
                                 '\\email',
                                 '\\institution',
                                 '\\streetaddress',
                                 '\\city',
                                 '\\country',
                                 '\\postcode',
                                 '\\ccsdesc',
                                 '\\received',
                                 '\\includegraphics',
                                 '\\caption',
                                 '\\centering',
                                 '\\label',
                                 '\\maketitle',
                                 '\\toprule',
                                 '\\multirow',
                                 '\\multicolumn',
                                 '\\cmidrule',
                                 '\\addlinespace',
                                 '\\midrule',
                                 '\\cellcolor',
                                 '\\bibliography',
                                 '}',
                                 '\\title',
                                 '</ccs2012>',
                                 '\\bottomrule',
                                 '<concept>',
                                 '<concept',
                                 '<ccs',
                                 '\\item',
                                 '</concept',
                                 '\\begin{abstract}',
                                 '\\end{abstract}',
                                 '\\endinput',
                                 '\\\\'
                                ]
        self.latex_begin_dictionary = [
                                       '\\begin{figure}',
                                       '\\begin{figure*}',
                                       '\\begin{equation}',
                                       '\\begin{CCSXML}',
                                       '\\begin{teaserfigure}',
                                       '\\begin{table*}',
                                       '\\begin{table}',
                                       '\\begin{gather}',
                                       '\\begin{align}',
                                      ]
        self.latex_end_dictionary = [
                                     '\\end{figure}',
                                     '\\end{figure*}',
                                     '\\end{equation}',
                                     '\\end{CCSXML}',
                                     '\\end{teaserfigure}',
                                     '\\end{table*}',
                                     '\\end{table}',
                                     '\\end{gather}',
                                     '\\end{align}',
                                    ]
        self._label_lines()


    def set_latex_dictonaries(self, begin_dictionary, end_dictionary, syntax_dictionary):
        """
        Set document specific dictionaries so that the lines could be labelled in accordance.


        Parameters
        ----------
        begin_dictionary     : list
                               Pythonic list containing latex syntax for begin commands (i.e. \\begin{align}).
        end_dictionary       : list
                               Pythonic list containing latex syntax for end commands (i.e. \\end{table}).
        syntax_dictionary    : list
                               Pythonic list containing latex syntax (i.e. \\item).

        """
        self.latex_begin_dictionary = begin_dictionary
        self.latex_end_dictionary = end_dictionary
        self.latex_dictionary = syntax_dictionary
        self._label_lines


    def _label_lines(self):
        """
        Internal function for labelling lines.
        """
        content_type_flag = False
        for line_id, line in enumerate(self.content):
            while len(line) > 0 and line[0] == ' ':
                 line = line[1::]
            self.content[line_id] = line
            if len(line) == 0:
                content_type = 'empty'
            elif line[0] == '%':
                content_type = 'comment'
            else:
                content_type = 'text'
            for syntax in self.latex_begin_dictionary:
                if line.find(syntax) != -1:
                    content_type_flag = True
                    content_type = 'latex'
            for syntax in self.latex_dictionary:
                if line.find(syntax) != -1:
                    content_type = 'latex'
            if content_type_flag == True:
                content_type = 'latex'
                for syntax in self.latex_end_dictionary:
                    if line.find(syntax) != -1:
                         content_type_flag = False
            self.content_type.append(content_type)


    def get_line_count(self):
        """
        Definition to get the line count.


        Returns
        -------
        line_count     : int
                         Number of lines in the loaded latex document.
        """
        self.line_count = len(self.content)
        return self.line_count


    def get_line(self, line_id = 0):
        """
        Definition to get a specific line by inputting a line nunber.


        Returns
        ----------
        line           : str
                         Requested line.
        content_type   : str
                         Line's content type (e.g., latex, comment, text).
        """
        line = self.content[line_id]
        content_type = self.content_type[line_id]
        return line, content_type

__init__(filename)

Parameters:

  • filename – 
           Source filename (i.e. sample.tex).
Source code in odak/tools/latex.py 
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def __init__(
             self,
             filename
            ):
    """
    Parameters
    ----------
    filename     : str
                   Source filename (i.e. sample.tex).
    """
    self.filename = filename
    self.content = read_text_file(self.filename)
    self.content_type = []
    self.latex_dictionary = [
                             '\\documentclass',
                             '\\if',
                             '\\pdf',
                             '\\else',
                             '\\fi',
                             '\\vgtc',
                             '\\teaser',
                             '\\abstract',
                             '\\CCS',
                             '\\usepackage',
                             '\\PassOptionsToPackage',
                             '\\definecolor',
                             '\\AtBeginDocument',
                             '\\providecommand',
                             '\\setcopyright',
                             '\\copyrightyear',
                             '\\acmYear',
                             '\\citestyle',
                             '\\newcommand',
                             '\\acmDOI',
                             '\\newabbreviation',
                             '\\global',
                             '\\begin{document}',
                             '\\author',
                             '\\affiliation',
                             '\\email',
                             '\\institution',
                             '\\streetaddress',
                             '\\city',
                             '\\country',
                             '\\postcode',
                             '\\ccsdesc',
                             '\\received',
                             '\\includegraphics',
                             '\\caption',
                             '\\centering',
                             '\\label',
                             '\\maketitle',
                             '\\toprule',
                             '\\multirow',
                             '\\multicolumn',
                             '\\cmidrule',
                             '\\addlinespace',
                             '\\midrule',
                             '\\cellcolor',
                             '\\bibliography',
                             '}',
                             '\\title',
                             '</ccs2012>',
                             '\\bottomrule',
                             '<concept>',
                             '<concept',
                             '<ccs',
                             '\\item',
                             '</concept',
                             '\\begin{abstract}',
                             '\\end{abstract}',
                             '\\endinput',
                             '\\\\'
                            ]
    self.latex_begin_dictionary = [
                                   '\\begin{figure}',
                                   '\\begin{figure*}',
                                   '\\begin{equation}'