PyOPIA 2.4.2__tar.gz → 2.4.4__tar.gz

{pyopia-2.4.2 → pyopia-2.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.4.2
+Version: 2.4.4
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.4.4/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.4.4'

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/background.py

@@ -8,7 +8,7 @@ def ini_background(bgfiles, load_function):
     '''
     Create and initial background stack and average image
 
-    Parameters:
+    Parameters
     -----------
     bgfiles : list
         List of strings of filenames to be used in background creation
@@ -39,7 +39,7 @@ def shift_bgstack_accurate(bgstack, imbg, imnew):
     The new background is calculated slowly by computing the mean of all images
     in the background stack.
 
-    Parameters:
+    Parameters
     -----------
     bgstack : list
         list of all images in the background stack
@@ -69,9 +69,9 @@ def shift_bgstack_fast(bgstack, imbg, imnew):
     adding the new image (both scaled by the stacklength).
     This is close to a running mean, but not quite.
 
-    Parameters:
+    Parameters
     -----------
-    bgstac : list
+    bgstack : list
         list of all images in the background stack
     imbg : uint8
         background image
@@ -102,7 +102,7 @@ def correct_im_accurate(imbg, imraw):
     There is a small chance of clipping of imc in both crushed blacks and blown
     highlights if the background or raw images are very poorly obtained
 
-    Parameters:
+    Parameters
     -----------
     imbg : float64
         background averaged image
@@ -131,7 +131,7 @@ def correct_im_fast(imbg, imraw):
     There is high potential for clipping of imc in both crushed blacks an blown
     highlights, especially if the background or raw images are not properly obtained
 
-    Parameters:
+    Parameters
     -----------
     imraw : array
         raw image
@@ -158,7 +158,7 @@ def shift_and_correct(bgstack, imbg, imraw, stacklength, real_time_stats=False):
 
     This is a wrapper for shift_bgstack and correct_im
 
-    Parameters:
+    Parameters
     -----------
     bgstack : list
         list of all images in the background stack
@@ -200,16 +200,11 @@ class CorrectBackgroundAccurate():
     to this class, and the skip_next_steps flag is set in the pipeline Data. No background correction
     is performed during these steps.
 
-    Pipeline input data:
-    --------------------
-    :class:`pyopia.pipeline.Data`
-
-        containing the following keys:
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.imraw`
 
-        :attr:`pyopia.pipeline.Data.imraw`
-
-    Parameters:
-    -----------
+    Parameters
+    ----------
     bgshift_function : (string, optional)
         Function used to shift the background. Defaults to passing (i.e. static background)
         Available options are 'accurate', 'fast', or 'pass' to apply a statick background correction:
@@ -225,9 +220,9 @@ class CorrectBackgroundAccurate():
         The key in Pipeline.data of the image to be background corrected.
         Defaults to 'imraw'
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.im_corrected`
@@ -237,11 +232,11 @@ class CorrectBackgroundAccurate():
 
         :attr:`pyopia.pipeline.Data.imbg`
 
-    Example pipeline uses:
-    ----------------------
+    Examples
+    --------
     Apply moving average using :func:`pyopia.background.shift_bgstack_accurate` :
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.correctbackground]
         pipeline_class = 'pyopia.background.CorrectBackgroundAccurate'
@@ -250,7 +245,7 @@ class CorrectBackgroundAccurate():
 
     Apply static background correction:
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.correctbackground]
         pipeline_class = 'pyopia.background.CorrectBackgroundAccurate'
@@ -311,21 +306,16 @@ class CorrectBackgroundNone():
     This simply makes `data['im_corrected'] = data['imraw'] in the pipeline.
     This simply makes `data['im_corrected'] = data['imraw'] in the pipeline.
 
-    Pipeline input data:
-    --------------------
-    :class:`pyopia.pipeline.Data`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.imraw`
 
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.imraw`
-
-    Parameters:
+    Parameters
     -----------
-    none
+    None
 
-    Returns:
+    Returns
     --------
-    :class:`pyopia.pipeline.Data`
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.im_corrected`
@@ -335,7 +325,7 @@ class CorrectBackgroundNone():
     ----------------------
     Don't apply any background correction after image load step :
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.nobackground]
         pipeline_class = 'pyopia.background.CorrectBackgroundNone'

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/classify.py

@@ -29,11 +29,13 @@ class Classify():
     A classifier class for PyOPIA workflow.
     This is intended as a parent class that can be used as a template for flexible classification methods
 
-    Args:
-        model_path=model_path (str)        : path to particle-classifier e.g.
-                                '/testdata/model_name/particle_classifier.h5'
+    Parameters
+    ----------
+    model_path : str
+        path to particle-classifier e.g. '/testdata/model_name/particle_classifier.keras'
 
-    Example:
+    Example
+    -------
 
     .. code-block:: python
 
@@ -41,7 +43,9 @@ class Classify():
 
         prediction = cl.proc_predict(roi) # roi is an image roi to be classified
 
-    Note that :meth:`Classify.load_model()`
+    Note
+    ----
+    :meth:`Classify.load_model()`
     is run when the :class:`Classify` class is initialised.
     If this is used in combination with multiprocessing then the model must be loaded
     on the process where it will be used and not passed between processers
@@ -49,20 +53,23 @@ class Classify():
 
     The config setup looks like this:
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.classifier]
         pipeline_class = 'pyopia.classify.Classify'
         model_path = 'keras_model.h5' # path to trained nn model
 
-    If `[steps.classifier]`is not defined, the classification will be skipped and no probabilities reported.
+    If '[steps.classifier]' is not defined, the classification will be skipped and no probabilities reported.
+
+    See Also
+    --------
 
     If you want to use an example trained model for SilCam data
-    (no guarantee of accuracy for other applications), you can get it using `exampledata`
-    within the notebooks folder (https://github.com/SINTEF/pyopia/blob/main/notebooks/exampledata.py):
+    (no guarantee of accuracy for other applications), you can get it using :mod:`pyopia.exampledata`:
 
     .. code-block:: python
 
+        import pyopia.exampledata
         model_path = exampledata.get_example_model()
 
     '''
@@ -80,8 +87,12 @@ class Classify():
         '''
         Load a trained Keras model into the Classify class.
 
-        self.model (tf model object) : loaded Keras model
-        self.class_names (list) : names for the model output classes
+        Parameters
+        ----------
+        model : tf model object
+            loaded Keras model
+        class_names: list
+            names for the model output classes
         '''
         model_path = self.model_path
 
@@ -112,11 +123,15 @@ class Classify():
         '''
         Preprocess ROI ready for prediction. example here based on the pysilcam network setup
 
-        Args:
-            img_input (float)        : a particle ROI before preprocessing with range 0-1
+        Parameters
+        ----------
+        img_input : float
+            A particle ROI before preprocessing with range 0-1
 
-        Returns:
-            img_preprocessed (float) : a particle ROI with range 0.-255., corrected and preprocessed, ready for prediction
+        Returns
+        -------
+        img_preprocessed : float
+            A particle ROI with range 0.-255., corrected and preprocessed, ready for prediction
         '''
 
         whitebalanced = np.copy(img_input).astype(np.float64)
@@ -153,12 +168,16 @@ class Classify():
         '''
         Use tensorflow model to classify particles. example here based on the pysilcam network setup.
 
-        Args:
-            img_preprocessed (float) : a particle ROI arry, corrected and preprocessed using :meth:`Classify.preprocessing`,
-                                       ready for prediction using :meth:`Classify.predict`
+        Parameters
+        ----------
+        img_preprocessed: float
+            A particle ROI arry, corrected and preprocessed using :meth:`Classify.preprocessing`,
+            ready for prediction using :meth:`Classify.predict`
 
-        Returns:
-            prediction (array)       : the probability of the roi belonging to each class
+        Returns
+        -------
+        prediction : array
+            The probability of the roi belonging to each class
         '''
 
         prediction = self.model(img_preprocessed, training=False)
@@ -170,11 +189,15 @@ class Classify():
         Run pre-processing (:meth:`Classify.preprocessing`) and prediction (:meth:`Classify.predict`)
         using tensorflow model to classify particles. example here based on the pysilcam network setup.
 
-        Args:
-            img_input (float)  : a particle ROI with range 0-1 before preprocessing
+        Parameters
+        ----------
+        img_input : float
+            Aparticle ROI with range 0-1 before preprocessing
 
-        Returns:
-            prediction (array) : the probability of the roi belonging to each class
+        Returns
+        -------
+        prediction : array
+            The probability of the roi belonging to each class
         '''
         img_preprocessed = self.preprocessing(img_input)
         prediction = self.predict(img_preprocessed)

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/instrument/common.py

@@ -7,21 +7,17 @@ import numpy as np
 class RectangularImageMask():
     '''PyOpia pipline-compatible class for masking out part of the raw image.
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-        containing the following keys:
+        Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.imraw`
 
-        :attr:`pyopia.pipeline.Data.imraw`
-
-    Parameters:
-    -----------
+    Parameters
+    ----------
     mask_bbox : (list, optional)
         Pixel corner coordinates of rectangle to mask (image outside the rectangle is set to 0)
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the new key:
 
         :attr:`pyopia.pipeline.Data.im_masked`
@@ -31,7 +27,7 @@ class RectangularImageMask():
     ----------------------
     Put this in your pipeline right after load step to mask out border outside specified pixel coordinates:
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.mask]
         pipeline_class = 'pyopia.instrument.common.RectangularImageMask'

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/instrument/holo.py

@@ -134,6 +134,9 @@ class Load():
 class Reconstruct():
     '''PyOpia pipline-compatible class for reconstructing a single holo image
 
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.im_corrected`
+
     Parameters
     ----------
     stack_clean : float
@@ -143,16 +146,9 @@ class Reconstruct():
     inverse_output_option :  int
         switch to control optional scaling of output intensity (0=square/default,1=linear)
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.im_corrected`
-
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.im_stack`
@@ -440,13 +436,8 @@ def find_focus_sobel(im_stack, bbox, increase_depth_of_field):
 class Focus():
     '''PyOpia pipline-compatible class for creating a focussed image from an image stack
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.im_stack`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.im_stack`
 
     Parameters
     ----------
@@ -631,8 +622,8 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
     output_prefix : str
         output_prefix
 
-    Returns:
-    --------
+    Returns
+    -------
     dict
         pipeline_config toml dict
     '''

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/instrument/silcam.py

@@ -11,10 +11,12 @@ from skimage.exposure import rescale_intensity
 def timestamp_from_filename(filename):
     '''get a pandas timestamp from a silcam filename
 
-    Args:
+    Parameters
+    ----------
         filename (string): silcam filename (.silc)
 
-    Returns:
+    Returns
+    -------
         timestamp: timestamp from pandas.to_datetime()
     '''
 
@@ -46,16 +48,12 @@ class SilCamLoad():
     and extracting the timestamp using
     :func:`pyopia.instrument.silcam.timestamp_from_filename`
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-        containing the following keys:
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.filename`
 
-        :attr:`pyopia.pipeline.Data.filename`
-
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.timestamp`
@@ -77,16 +75,12 @@ class SilCamLoad():
 class ImagePrep():
     '''PyOpia pipline-compatible class for preparing silcam images for further analysis
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-        containing the following keys:
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.img`
 
-        :attr:`pyopia.pipeline.Data.img`
-
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.im_minimum`
@@ -120,8 +114,8 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
     output_prefix : str
         output_prefix
 
-    Returns:
-    --------
+    Returns
+    -------
     dict
         pipeline_config toml dict
     '''

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/instrument/uvp.py

@@ -11,10 +11,12 @@ import skimage.io
 def timestamp_from_filename(filename):
     '''get a pandas timestamp from a UVP vignette image filename
 
-    Args:
+    Parameters
+    ----------
         filename (string): UVP filename (.png)
 
-    Returns:
+    Returns
+    -------
         timestamp: timestamp from pandas.to_datetime()
     '''
 
@@ -48,16 +50,12 @@ class UVPLoad():
     and extracting the timestamp using
     :func:`pyopia.instrument.uvp.timestamp_from_filename`
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.filename`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.filename`
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.timestamp`
@@ -90,8 +88,8 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
     output_prefix : str
         output_prefix
 
-    Returns:
-    --------
+    Returns
+    -------
     dict
         pipeline_config toml dict
     '''

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/io.py

@@ -314,12 +314,14 @@ class StatsToDisc():
 
     Returns
     -------
-    data : dict
-        data from pipeline
+    data : :class:`pyopia.pipeline.Data`
+        data from the pipeline
 
+    Example
+    -------
     Example config for pipeline useage:
 
-    .. code-block:: python
+    .. code-block:: toml
 
         [steps.output]
         pipeline_class = 'pyopia.io.StatsToDisc'

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/pipeline.py

@@ -1,7 +1,7 @@
 '''
 Module for managing the PyOpia processing pipeline
 
-Refer to :class:`Pipeline` for examples of how to process datasets and images
+Refer to the :class:`Pipeline` class documentation for examples of how to process datasets and images
 '''
 from typing import TypedDict
 import datetime
@@ -18,15 +18,15 @@ logger = logging.getLogger()
 
 class Pipeline():
     '''The processing pipeline class
-    ================================
 
+    Note
+    ----
     The classes called in the Pipeline steps can be modified, and the names of the steps changed.
     New steps can be added or deleted as required.
 
     The classes called in the Pipeline steps need to take a TOML-formatted dictionary as input
-    and return a dictionary of data as output.
-    This common data dictionary: :class:`pyopia.pipeline.Data` is therefore passed between steps so that data
-    or variables generated by each step can be passed along the pipeline.
+    and return a dictionary of data as output. This common data dictionary: :class:`pyopia.pipeline.Data`
+    is therefore passed between steps so that data or variables generated by each step can be passed along the pipeline.
 
     By default, the step names: `initial`, `classifier`, and `createbackground`
     are run when initialising `Pipeline`.
@@ -38,15 +38,15 @@ class Pipeline():
     The step called 'classifier' must return a dict containing:
     :attr:`pyopia.pipeline.Data.cl` in order to run successfully.
 
-    Running a pipeline:
-    """""""""""""""""""
-
-    `Pipeline.run()` takes a string as input.
-    This string is put into the `data` dict available to the steps in the pipeline as `data['filename']`.
+    :func:`Pipeline.run()` takes a string as input.
+    This string is put into :class:`pyopia.pipeline.Data`, available to the steps in the pipeline as `data['filename']`.
     This is intended for use in looping through several files during processing, so run can be
     called multiple times with different filenames.
 
-    Examples of setting up and running a pipeline,
+    Examples
+    --------
+
+    Examples of setting up and running a pipeline
     can be found for SilCam `here <https://github.com/SINTEF/pyopia/blob/main/notebooks/pipeline-holo.ipynb>`_,
     and holographic analysis `here <https://github.com/SINTEF/pyopia/blob/main/notebooks/pipeline-holo.ipynb>`_.
 
@@ -54,7 +54,7 @@ class Pipeline():
     and for holographic analysis `here <https://github.com/SINTEF/pyopia/blob/main/notebooks/config-holo.toml>`_.
 
     You can check the workflow used by reading the steps from the metadata in the
-    output file using :func:`pyopia.pipeline.steps_from_xstats`
+    output file using :func:`pyopia.io.steps_from_xstats`
 
     More examples and guides can be found on the `PyOIA By Example <https://pyopia.readthedocs.io/en/latest/examples.html>`_ page.
     '''
@@ -94,11 +94,13 @@ class Pipeline():
         stats : DataFrame
             particle statistics associated with 'filename'
 
-        Note: the returned stats from this function are single-image only and not appended
+        Note
+        ----
+        The returned stats from this function are single-image only and not appended
         if you loop through several filenames! It is recommended to use this step in the pipeline
         for properly appending data into NetCDF format when processing several files.
 
-        .. code-block:: python
+        .. code-block:: toml
 
             [steps.output]
             pipeline_class = 'pyopia.io.StatsDisc'
@@ -187,15 +189,6 @@ class Pipeline():
 
 class Data(TypedDict):
     '''Data dictionary which is passed between :class:`pyopia.pipeline` steps.
-
-    For debugging, you can use :class:`pyopia.pipeline.ReturnData`
-    at the end of a steps dictionary to return of this Data dictionary
-    for exploratory purposes.
-
-    In future this may be better as a data class with slots (from python 3.10).
-
-    This is an example of a link to the imc key doc:
-    :attr:`pyopia.pipeline.Data.im_corrected`
     '''
 
     raw_files: str
@@ -335,16 +328,16 @@ def build_steps(toml_steps):
 
 
 class FilesToProcess:
-    def __init__(self, glob_pattern=None):
-        '''Build file list from glob pattern if specified.
-           Create FilesToProcess.chunked_files is chunks specified
-           File list from glob will be sorted.
+    '''Build file list from glob pattern if specified.
+    Create FilesToProcess.chunked_files is chunks specified
+    File list from glob will be sorted.
 
-        Parameters
-        ----------
-        glob_pattern : str, optional
-            Glob pattern, by default None
-        '''
+    Parameters
+    ----------
+    glob_pattern : str, optional
+        Glob pattern, by default None
+    '''
+    def __init__(self, glob_pattern=None):
         self.files = None
         self.background_files = []
         self.chunked_files = []
@@ -382,7 +375,7 @@ class FilesToProcess:
 
         Parameters
         ----------
-        chunks : int
+        num_chunks : int
             number of chunks to produce (must be at least 1)
         '''
         if num_chunks < 1:
@@ -404,8 +397,12 @@ class FilesToProcess:
             chunk = [chunk.insert(0, bg_file) for bg_file in reversed(self.background_files[-average_window:])]
 
     def build_initial_background_files(self, average_window=0):
-        '''
-        Create a list of files to use for initializing the background in the first chunk
+        '''Create a list of files to use for initializing the background in the first chunk
+
+        Parameters
+        ----------
+        average_window : int, optional
+            number of images to use in creating a background, by default 0
         '''
         self.background_files = []
         for f in self.files[0:average_window]:

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/process.py

@@ -481,15 +481,10 @@ def statextract(imbw, timestamp, imc,
 class Segment():
     '''PyOpia pipline-compatible class for calling segment
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.im_corrected`
 
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.im_corrected`
-
-    Parameters:
+    Parameters
     ----------
     minimum_area : (int, optional)
         minimum number of pixels for particle detection. Defaults to 12.
@@ -501,9 +496,9 @@ class Segment():
         The key in Pipeline.data of the image to be segmented.
         Defaults to 'im_corrected'
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.imbw`
@@ -529,19 +524,12 @@ class Segment():
 class CalculateStats():
     '''PyOpia pipline-compatible class for calling statextract
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.imbw`
-
-        :attr:`pyopia.pipeline.Data.timestamp`
-
-        :attr:`pyopia.pipeline.Data.cl`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.imbw`
+        - :attr:`pyopia.pipeline.Data.timestamp`
+        - :attr:`pyopia.pipeline.Data.cl`
 
-    Parameters:
+    Parameters
     ----------
     max_coverage : (int, optional)
         percentage of the image that is allowed to be filled by particles. Defaults to 30.
@@ -560,9 +548,9 @@ class CalculateStats():
         Key of an image in Pipeline.data that is used for outputting ROIs and passing to the classifier.
         Defaults to 'im_corrected'
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.stats`
@@ -606,23 +594,17 @@ class CalculateStats():
 class CalculateImageStats():
     '''PyOpia pipline-compatible class for collecting whole-image statistics
 
-    Pipeline input data:
-    ---------
-    :class:`pyopia.pipeline.Data`
-
-        containing the following keys:
-
-        :attr:`pyopia.pipeline.Data.stats`
-
-        :attr:`pyopia.pipeline.Data.timestamp`
+    Required keys in :class:`pyopia.pipeline.Data`:
+        - :attr:`pyopia.pipeline.Data.stats`
+        - :attr:`pyopia.pipeline.Data.timestamp`
 
-    Parameters:
+    Parameters
     ----------
     None
 
-    Returns:
-    --------
-    :class:`pyopia.pipeline.Data`
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
         containing the following new keys:
 
         :attr:`pyopia.pipeline.Data.image_stats`

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/simulator/silcam.py

@@ -15,15 +15,7 @@ from pyopia.pipeline import Pipeline
 
 
 class SilcamSimulator():
-    def __init__(self, total_volume_concentration=1000,
-                 d50=1000,
-                 MinD=10,
-                 PIX_SIZE=28,
-                 PATH_LENGTH=40,
-                 imx=2048,
-                 imy=2448,
-                 nims=50):
-        '''SilCam simulator
+    '''SilCam simulator
 
         Parameters
         ----------
@@ -44,20 +36,28 @@ class SilcamSimulator():
         nims : int, optional
             number of images to simulate, by default 50
 
-        Example:
-        --------
+        Example
+        -------
 
-        ```python
-        from pyopia.simulator.silcam import SilcamSimulator
+        .. code-block:: python
 
-        sim = SilcamSimulator()
-        sim.check_convergence()
-        sim.synthesize()
-        sim.process_synthetic_image()
-        sim.plot()
-        ```
+            from pyopia.simulator.silcam import SilcamSimulator
 
-        '''
+            sim = SilcamSimulator()
+            sim.check_convergence()
+            sim.synthesize()
+            sim.process_synthetic_image()
+            sim.plot()
+
+    '''
+    def __init__(self, total_volume_concentration=1000,
+                 d50=1000,
+                 MinD=10,
+                 PIX_SIZE=28,
+                 PATH_LENGTH=40,
+                 imx=2048,
+                 imy=2448,
+                 nims=50):
         self.total_volume_concentration = total_volume_concentration
         self.d50 = d50
         self.MinD = MinD
@@ -97,7 +97,7 @@ class SilcamSimulator():
         '''Check statistical convergence of randomly selected size distributions
         over the `nims`number of images
 
-        Attributes added by method
+        Parameters
         ----------
         data['volume_distribution'] : array
             volume distribution of shape (nims, dias)
@@ -164,7 +164,7 @@ class SilcamSimulator():
     def synthesize(self):
         '''Synthesize an image and measure droplets
 
-        Attributes added by method
+        Parameters
         ----------
         data['synthetic_image_data']['image'] : array
             synthetic image
@@ -205,7 +205,7 @@ class SilcamSimulator():
     def process_synthetic_image(self):
         '''Put the synthetic image `data['synthetic_image_data']['image']` through a basic pyopia processing pipeline
 
-        Attributes added by method
+        Parameters
         ----------
         data['synthetic_image_data']['pyopia_processed_volume_distribution'] : array
             pyopia processed volume distribution associated with `dias`size classes

{pyopia-2.4.2 → pyopia-2.4.4}/pyopia/statistics.py

@@ -523,7 +523,8 @@ def get_j(dias, number_distribution):
     number_distribution : array
         number distribution in number per micron per litre
 
-    Returns:
+    Returns
+    -------
     junge_slope : float
         Junge slope from fitting of psd between 150 and 300um
     '''
@@ -977,7 +978,8 @@ def vd_to_nd(volume_distribution, dias):
 def vd_to_nc(volume_distribution, dias):
     '''calculate number concentration from volume distribution
 
-    Args:
+    Parameters
+    ----------
     volume_distribution : array
         particle volume distribution calculated from vd_from_stats()
     dias : array

pyopia-2.4.2/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.4.2'