partial doc of analyzer components

doc/api.rst

@@ -15,5 +15,6 @@ The recommended starting point is :mod:`tramway.helper`.
     tramway.inference
     tramway.feature
     tramway.utils
+    tramway.analyzer
 
 

doc/deconvolution.rst

@@ -1,3 +1,4 @@
+.. _deconvolution:
 
 The :mod:`~tramway.deconvolution` module adds several dependencies, including *scikit-image>=0.14.2*, *tifffile* and *tensorflow*. *keras* is optional as it is now included in *tensorflow* releases.
 

doc/tramway.analyzer.rst

@@ -0,0 +1,113 @@
+
+tramway.analyzer package
+========================
+
+.. automodule:: tramway.analyzer
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.spt_data package
+---------------------------------
+
+.. automodule:: tramway.analyzer.spt_data
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.roi package
+----------------------------
+
+.. automodule:: tramway.analyzer.roi
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.time package
+-----------------------------
+
+.. automodule:: tramway.analyzer.time
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.tesseller package
+----------------------------------
+
+.. automodule:: tramway.analyzer.tesseller
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.tesseller.stdalg module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This module is exported by the :mod:`tramway.analyzer` package
+as *tessellers*.
+
+.. automodule:: tramway.analyzer.tesseller.stdalg
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.tesseller.post package
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: tramway.analyzer.tesseller.post
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.tesseller.post.merger module
+"""""""""""""""""""""""""""""""""""""""""""""
+
+This module is exported by the :mod:`tramway.analyzer` package
+as *cell_mergers*.
+
+.. automodule:: tramway.analyzer.tesseller.post.merger
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.sampler package
+--------------------------------
+
+.. automodule:: tramway.analyzer.sampler
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.mapper package
+-------------------------------
+
+.. automodule:: tramway.analyzer.mapper
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.pipeline package
+---------------------------------
+
+.. automodule:: tramway.analyzer.pipeline
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.env package
+----------------------------
+
+.. automodule:: tramway.analyzer.env
+    :members:
+    :show-inheritance:
+
+
+tramway.analyzer.env.environments module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This module is exported by the :mod:`tramway.analyzer` package
+as *environments*.
+
+.. automodule:: tramway.analyzer.env.environments
+    :members:
+    :show-inheritance:
+

tramway/analyzer/__init__.py

@@ -178,42 +178,79 @@ def logger(self, logger):
         self._logger = logger
 
     def _get_spt_data(self):
+        """
+        SPT data accessor.
+
+        See :class:`~spt_data.SPTDataInitializer`.
+        """
         return self._spt_data
     def _set_spt_data(self, data):
         self._spt_data = data
     spt_data = selfinitializing_property('spt_data', _get_spt_data, _set_spt_data, SPTData)
 
     def _get_roi(self):
+        """
+        ROI accessor.
+
+        See :class:`~roi.ROIInitializer`.
+        """
         return self._roi
     def _set_roi(self, roi):
         self._roi = roi
     roi = selfinitializing_property('roi', _get_roi, _set_roi, ROI)
 
     def _get_time(self):
+        """
+        Time segmentation procedure.
+
+        See :class:`~time.TimeInitializer`.
+        """
         return self._time
     def _set_time(self, time):
         self._time = time
     time = selfinitializing_property('time', _get_time, _set_time, Time)
 
     def _get_tesseller(self):
+        """
+        Tessellation procedure.
+
+        See :class:`~tesseller.TessellerInitializer`.
+        """
         return self._tesseller
     def _set_tesseller(self, tesseller):
         self._tesseller = tesseller
     tesseller = selfinitializing_property('tesseller', _get_tesseller, _set_tesseller, Tesseller)
 
     def _get_sampler(self):
+        """
+        Sampling procedure.
+
+        See :class:`~sampler.SamplerInitializer`.
+        """
         return self._sampler
     def _set_sampler(self, sampler):
         self._sampler = sampler
     sampler = selfinitializing_property('sampler', _get_sampler, _set_sampler, Sampler)
 
     def _get_mapper(self):
+        """
+        Inference procedure.
+
+        See :class:`~mapper.MapperInitializer`.
+        """
         return self._mapper
     def _set_mapper(self, mapper):
         self._mapper = mapper
     mapper = selfinitializing_property('mapper', _get_mapper, _set_mapper, Mapper)
 
     def _get_env(self):
+        """
+        Environment backend for operating the pipeline.
+
+        If not set, the pipeline will run locally in the current interpreter.
+
+        See :mod:`~env.environments`.
+        """
         return self._env
     def _set_env(self, env):
         self._env = env
@@ -238,9 +275,17 @@ def __init__(self):
 
     @property
     def pipeline(self):
+        """
+        Parallelization scheme.
+
+        See `env`.
+        """
         return self._pipeline
 
     def run(self):
+        """
+        launches the pipeline.
+        """
         return self.pipeline.run()
 
     def __setattr__(self, attrname, obj):

tramway/analyzer/pipeline/__init__.py

@@ -37,7 +37,7 @@ class Pipeline(AnalyzerNode):
     `pipeline` attribute of an :class:`~tramway.analyzer.RWAnalyzer` object.
 
     The main methods are `append_stage` and `run`.
-    Note that the `run` method is called by :met:`~tramway.analyzer.RWAnalyzer.run`
+    Note that the `run` method is called by :meth:`~tramway.analyzer.RWAnalyzer.run`
     of :class:`~tramway.analyzer.RWAnalyzer`.
     """
     __slots__ = ('_stage',)

tramway/analyzer/roi/__init__.py

@@ -53,6 +53,7 @@ class IndividualROI(BaseRegion):
     pass
 
 class BoundingBox(IndividualROI):
+    """ See :class:`BoundingBoxes`. """
     __slots__ = ('_bounding_box',)
     def __init__(self, bb, label, spt_data, **kwargs):
         IndividualROI.__init__(self, spt_data, label, **kwargs)
@@ -67,6 +68,9 @@ def bounding_box(self):
         return self._bounding_box
 
 class SupportRegion(BaseRegion):
+    """
+    union of overlapping ROI.
+    """
     __slots__ = ('_sr_index','_support_regions')
     def __init__(self, r, regions, spt_data, **kwargs):
         BaseRegion.__init__(self,
@@ -89,12 +93,19 @@ def bounding_box(self):
             return np.min(np.stack(minima, axis=0), axis=0), np.max(np.stack(maxima, axis=0), axis=0)
 
 class FullRegion(BaseRegion):
+    """
+    supplies with the full dataset; does not actually crop.
+    """
     __slots__ = ()
     def crop(self, df=None):
         return self._spt_data.dataframe if df is None else df
 
 
 class DecentralizedROIManager(AnalyzerNode):
+    """
+    This class allows to iterate over the ROI defined at the level of
+    each SPT data item.
+    """
     __slots__ = ('_records',)
     def __init__(self, first_record=None, **kwargs):
         AnalyzerNode.__init__(self, **kwargs)
@@ -145,6 +156,12 @@ def as_support_regions(self, index=None, source=None, **kwargs):
 
 
 class ROIInitializer(Initializer):
+    """
+    initial value for the `RWAnalyzer.roi` attribute.
+
+    `from_...` methods alters the parent attribute which specializes
+    into an initialized :class:`.abc.ROI` object.
+    """
     __slots__ = ()
     def specialize(self, cls, *args, **kwargs):
         Initializer.specialize(self, cls, *args, **kwargs)
@@ -166,8 +183,14 @@ def _from_common_roi(self, roi):
     def _register_decentralized_roi(self, roi):
         self.specialize( DecentralizedROIManager, roi )
     def from_bounding_boxes(self, bb, label=None, group_overlapping_roi=False):
+        """
+        Defines ROI as bounding boxes.
+        """
         self.specialize( BoundingBoxes, bb, label, group_overlapping_roi )
     def from_squares(self, centers, side, label=None, group_overlapping_roi=False):
+        """
+        Defines ROI as centers for squares/cubes of uniform size.
+        """
         bb = [ (center-.5*side, center+.5*side) for center in centers ]
         self.from_bounding_boxes(bb, label, group_overlapping_roi)
     ## in the case no ROI are defined
@@ -211,6 +234,9 @@ def as_individual_roi(self, index=None, collection=None, source=None, **kwargs):
 
 
 class CommonROI(AnalyzerNode):
+    """
+    Mirrors the global `RWAnalyzer.roi` attribute.
+    """
     __slots__ = ('_global',)
     def __init__(self, roi, parent=None):
         AnalyzerNode.__init__(self, parent)
@@ -232,6 +258,9 @@ def as_individual_roi(self, index=None, collection=None, source=None, return_ind
 
 
 class SpecializedROI(AnalyzerNode):
+    """
+    Base class for initialized *roi* attributes.
+    """
     __slots__ = ('_global','_collections')
     def __init__(self, **kwargs):
         AnalyzerNode.__init__(self, **kwargs)
@@ -328,6 +357,9 @@ def bear_child(i, *args):
 
 
 class HasROI(AnalyzerNode):
+    """ Class to be inherited from by SPT data item classes.
+    
+    Maintains a self-modifying *roi* attribute."""
     __slots__ = ('_roi',)
     def _get_roi(self):
         return self._roi
@@ -338,6 +370,7 @@ def _set_roi(self, roi):
             assert isinstance(global_roi_attr, DecentralizedROIManager)
         global_roi_attr._register_decentralized_roi(self)
     roi = selfinitializing_property('roi', _get_roi, _set_roi, ROI)
+
     def __init__(self, roi=ROIInitializer, **kwargs):
         AnalyzerNode.__init__(self, **kwargs)
         self._roi = roi(self._set_roi, parent=self)