BoundingBoxes.to_ascii_file + bugfix in NonTrackingTracker.track for …

…raw dataframes + source argument in Tracker.track + roi.utils.{epanechnikov_density,density_based_roi}

doc/tramway.analyzer.rst

@@ -4,7 +4,6 @@ tramway.analyzer package
 
 .. automodule:: tramway.analyzer
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -14,7 +13,6 @@ tramway.analyzer.artefact package
 
 .. automodule:: tramway.analyzer.artefact
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -23,7 +21,6 @@ tramway.analyzer.attribute package
 
 .. automodule:: tramway.analyzer.attribute
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -32,7 +29,6 @@ tramway.analyzer.images package
 
 .. automodule:: tramway.analyzer.images
     :members:
-    :undoc-members:
     :show-inheritance:
     :private-members: _RawImage
 
@@ -59,7 +55,6 @@ tramway.analyzer.tracker package
 
 .. automodule:: tramway.analyzer.tracker
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -69,7 +64,6 @@ tramway.analyzer.spt_data package
 
 .. automodule:: tramway.analyzer.spt_data
     :members:
-    :undoc-members:
     :show-inheritance:
     :private-members: _SPTDataFrame
 
@@ -87,7 +81,6 @@ tramway.analyzer.roi package
 
 .. automodule:: tramway.analyzer.roi
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -97,7 +90,6 @@ tramway.analyzer.tesseller package
 
 .. automodule:: tramway.analyzer.tesseller
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -107,7 +99,6 @@ tramway.analyzer.tesseller.proxy module
 
 .. automodule:: tramway.analyzer.tesseller.proxy
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -119,7 +110,6 @@ as *tessellers*.
 
 .. automodule:: tramway.analyzer.tesseller.proxied
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -128,7 +118,6 @@ tramway.analyzer.tesseller.plugin module
 
 .. automodule:: tramway.analyzer.tesseller.plugin
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -148,7 +137,6 @@ as *cell_mergers*.
 
 .. automodule:: tramway.analyzer.tesseller.post.merger
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -165,7 +153,6 @@ tramway.analyzer.time package
 
 .. automodule:: tramway.analyzer.time
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -175,7 +162,6 @@ tramway.analyzer.sampler package
 
 .. automodule:: tramway.analyzer.sampler
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -185,7 +171,6 @@ tramway.analyzer.mapper package
 
 .. automodule:: tramway.analyzer.mapper
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -203,7 +188,6 @@ tramway.analyzer.pipeline package
 
 .. automodule:: tramway.analyzer.pipeline
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -212,7 +196,6 @@ tramway.analyzer.env package
 
 .. automodule:: tramway.analyzer.env
     :members:
-    :undoc-members:
     :show-inheritance:
     :member-order: bysource
 
@@ -225,7 +208,6 @@ as *environments*.
 
 .. automodule:: tramway.analyzer.env.environments
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
@@ -234,6 +216,5 @@ tramway.analyzer.browser package
 
 .. automodule:: tramway.analyzer.browser
     :members:
-    :undoc-members:
     :show-inheritance:
 

tests/test_analyzer.py

@@ -2,6 +2,7 @@
 import os
 from math import *
 import numpy
+import pandas
 import random
 import subprocess
 import pytest
@@ -249,17 +250,17 @@ def test_3roi_hexagons(self, one_sptdatafile, tmpdir):
         self.tmpdir = tmpdir
         self.label = '3roi_hexagons'
         #
-        roi = [([-.4,-.5],[0.,-.1]),([-.1,0.],[.3,.4]),([.1,-.3],[.5,.1])]
-        roi = [ (numpy.array(lb), numpy.array(ub)) for lb, ub in roi ]
+        roi_bounds = [([-.4,-.5],[0.,-.1]),([-.1,0.],[.3,.4]),([.1,-.3],[.5,.1])]
+        roi_bounds = [ (numpy.array(lb), numpy.array(ub)) for lb, ub in roi_bounds ]
         #
         a=RWAnalyzer()
         a.spt_data.from_ascii_file(one_sptdatafile)
         a.tesseller.from_callable(tessellers.Hexagons)
         a.tesseller.ref_distance = .01
         a.tesseller.avg_location_count = 5
-        a.roi.from_bounding_boxes(roi, label='3-roi hexagons', group_overlapping_roi=True)
+        a.roi.from_bounding_boxes(roi_bounds, label='3-roi hexagons', group_overlapping_roi=True)
         b = RoiHelper(one_sptdatafile, verbose=False)
-        b.set_bounding_boxes(roi, collection_label='3-roi hexagons')
+        b.set_bounding_boxes(roi_bounds, collection_label='3-roi hexagons')
         b.tessellate('hexagon', ref_distance=.01, avg_location_count=5)
         for i, r in enumerate(a.roi.as_support_regions()):
             df = r.crop()
@@ -416,8 +417,8 @@ def test_nooverlap_roi(self, dynamicmesh):
         a=RWAnalyzer()
         a.spt_data.from_ascii_file(dynamicmesh)
         a.spt_data.localization_precision = 1e-4
-        roi = [[.2,-.1],[-.3,.3],[0.,.1],[-.2,-0.]]
-        a.roi.from_squares(np.array(roi), .2, group_overlapping_roi=False)
+        roi_centers = [[.2,-.1],[-.3,.3],[0.,.1],[-.2,-0.]]
+        a.roi.from_squares(np.array(roi_centers), .2, group_overlapping_roi=False)
         #
         for i, r in a.roi.as_individual_roi(index=1, return_index=True):
             assert i == 1
@@ -454,8 +455,8 @@ def test_overlapping_roi(self, dynamicmesh):
         a=RWAnalyzer()
         a.spt_data.from_ascii_file(dynamicmesh)
         a.spt_data.localization_precision = 1e-4
-        roi = [[.2,-.1],[-.3,.3],[0.,.1],[-.2,-0.]]
-        a.roi.from_squares(np.array(roi), .2, group_overlapping_roi=True)
+        roi_centers = [[.2,-.1],[-.3,.3],[0.,.1],[-.2,-0.]]
+        a.roi.from_squares(np.array(roi_centers), .2, group_overlapping_roi=True)
         #
         j = 0
         for i,r in a.roi.as_individual_roi(return_index=True):
@@ -567,3 +568,20 @@ def test_init_for_misplaced_attributes(self):
                 else:
                     assert attr is not attr # could set the attribute before initializing its parent
 
+
+class TestSideEffects(object):
+    def test_attribute_overwrite(self):
+        warnings.simplefilter('ignore', SideEffectWarning)
+        a = RWAnalyzer()
+        a.spt_data.from_dataframe(pandas.DataFrame([], columns=list('xyt')))
+        a.spt_data.localization_precision = .03
+        a.spt_data.frame_interval = .05
+        a.time.frame_interval = .04
+        old_spt_data = a.spt_data
+        a.spt_data = spt_data.from_dataframe(pandas.DataFrame([], columns=list('xyt')))
+        a.spt_data.localization_error = old_spt_data.localization_error
+        a.spt_data.dt = old_spt_data.dt
+        assert a.spt_data.localization_precision == .03
+        assert a.spt_data.dt == .04
+        warnings.simplefilter('error', SideEffectWarning)
+

tramway/analyzer/__init__.py

@@ -12,12 +12,12 @@
 # knowledge of the CeCILL license and that you accept its terms.
 
 
-from tramway.core.exceptions import MisplacedAttributeWarning
-from warnings import warn
+from tramway.core.exceptions import MisplacedAttributeWarning, SideEffectWarning
+import warnings
 import logging
 
 def report_misplaced_attribute(attr_name, proper_parent_name):
-    warn('`{}` is an attribute of the initialized `{}` attribute; this warning message can safely be silenced'.format(attr_name, proper_parent_name), MisplacedAttributeWarning)
+    warnings.warn('`{}` is an attribute of the initialized `{}` attribute; this warning message can safely be silenced'.format(attr_name, proper_parent_name), MisplacedAttributeWarning)
 def proper_parent_name(attr_name):
     parent_name = None
     get_conditions, set_conditions = {}, {}
@@ -29,6 +29,9 @@ def proper_parent_name(attr_name):
         parent_name = 'tesseller'
     return parent_name, get_conditions, set_conditions
 
+warnings.filterwarnings('error', category=SideEffectWarning)
+
+
 from .attribute import *
 from .artefact  import *
 from .spt_data  import *
@@ -44,6 +47,15 @@ def proper_parent_name(attr_name):
 from .localizer import *
 from .tracker   import *
 
+import tramway.analyzer.spt_data.allsymbols  as spt_data
+import tramway.analyzer.roi.allsymbols       as roi
+import tramway.analyzer.time.allsymbols      as time
+import tramway.analyzer.tesseller.allsymbols as tesseller
+import tramway.analyzer.sampler.allsymbols   as sampler
+import tramway.analyzer.mapper.allsymbols    as mapper
+import tramway.analyzer.images.allsymbols    as images
+import tramway.analyzer.tracker.allsymbols   as tracker
+
 
 class BasicLogger(object):
     """
@@ -434,11 +446,22 @@ def __setattr__(self, attrname, obj):
                 attrname in ('script',):
             object.__setattr__(self, attrname, obj)
         elif callable(obj):
-            attr = getattr(self, attrname)
-            try:
-                attr.from_callable(obj)
-            except AttributeError:
-                raise AttributeError('attribute is read-only')
+            if attrname[0] != '_' and isinstance(obj, InitializerMethod):
+                attr = getattr(self, attrname)
+                if isinstance(attr, Initializer):
+                    obj.assign( self )
+                else:
+                    warnings.warn(
+                            "attribute '{}' is already initialized; side effects may occur".format(
+                                attrname),
+                            SideEffectWarning)
+                    obj.reassign( self )
+            else:
+                attr = getattr(self, attrname)
+                try:
+                    attr.from_callable(obj)
+                except AttributeError:
+                    raise AttributeError('attribute is read-only')
         else:
             parent_name, _, set_conditions = proper_parent_name(attrname)
             if parent_name is None:
@@ -461,8 +484,13 @@ def __getattr__(self, attrname):
 
 
 __all__ = ['RWAnalyzer',
+        'spt_data', 'roi',
+        'time', 'tesseller', 'sampler',
+        'mapper',
+        'images', 'tracker',
         'tessellers', 'cell_mergers',
         'Analysis', 'commit_as_analysis',
         'environments',
-        'first', 'single']
+        'first', 'single',
+        'SideEffectWarning']
 

tramway/analyzer/attribute/__init__.py

@@ -71,6 +71,9 @@ def initializer(self, cls):
         if cls is None:
             setter(self, None)
         elif callable(cls):
+            if isinstance(cls, InitializerMethod):
+                cls.assign( self )
+                return
             if metacls:
                 def typechecked_setter(obj):
                     if not isinstance(obj, metacls):
@@ -235,3 +238,38 @@ def __setattr__(self, attrname, val):
             setattr(self._proxied, attrname, val)
 
 
+__all__.append('InitializerMethod')
+class InitializerMethod(object):
+    """
+    Useful for explicit typing.
+    """
+    __slots__ = ('attrname', 'method', 'args', 'kwargs')
+    def __init__(self, method, attrname=None):
+        self.method = method
+        if attrname is None:
+            attrname = method.__module__.split('.')[-1]
+        self.attrname = attrname
+        self.args = self.kwargs = None
+    def __call__(self, *args, **kwargs):
+        self.args = args
+        self.kwargs = kwargs
+        return self
+    def assign(self, parent_analyzer):
+        if not (isinstance(self.args, tuple) and isinstance(self.kwargs, dict)):
+            raise RuntimeError('initializer method has not been called')
+        parent_attribute = getattr(parent_analyzer, self.attrname)
+        self.method(parent_attribute, *self.args, **self.kwargs)
+    def reassign(self, parent_analyzer):
+        import importlib
+        mod = importlib.import_module(self.method.__module__)
+        try:
+            clsname = str(self.method)[::-1].split('.', 1)[-1][::-1].split()[-1]
+            cls = getattr(mod, clsname)
+            assert isinstance(cls, type) and issubclass(cls, Initializer)
+        except:
+            raise AttributeError("cannot find a proper initializer for the '{}' attribute".format(self.attrname))
+        attr = getattr(type(parent_analyzer), self.attrname)
+        # TODO: add a freset method to the properties returned by selfinitializing_property
+        attr.fset(parent_analyzer, cls)
+        self.assign( parent_analyzer )
+

tramway/analyzer/env/environments.py

@@ -1347,7 +1347,7 @@ def wait_for_job_completion(self):
                     if _continue:
                         continue
                     if start is None:
-                        total = pending = None
+                        total, pending = None, 0
                     else:
                         total = stop
                         pending = stop - start

tramway/analyzer/images/allsymbols.py

@@ -0,0 +1,7 @@
+
+from . import *
+from ..attribute import InitializerMethod
+
+from_tiff_file  = InitializerMethod( ImagesInitializer.from_tiff_file  )
+from_tiff_files = InitializerMethod( ImagesInitializer.from_tiff_files )
+

tramway/analyzer/mapper/allsymbols.py

@@ -0,0 +1,7 @@
+
+from . import *
+from ..attribute import InitializerMethod
+
+from_plugin   = InitializerMethod( MapperInitializer.from_plugin   )
+from_callable = InitializerMethod( MapperInitializer.from_callable )
+