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[Pyphant-devel] SF.net SVN: pyphant:[622] trunk/src
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From: <zk...@us...> - 2009-03-17 14:26:47
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Revision: 622
http://pyphant.svn.sourceforge.net/pyphant/?rev=622&view=rev
Author: zklaus
Date: 2009-03-17 14:26:25 +0000 (Tue, 17 Mar 2009)
Log Message:
-----------
These are the documentation patches.
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/DataContainer.py
trunk/src/pyphant/pyphant/core/FieldContainer.py
trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
trunk/src/workers/OSC/OSC/AddColumn.py
trunk/src/workers/OSC/OSC/CompareFields.py
trunk/src/workers/OSC/OSC/ComputeFunctional.py
trunk/src/workers/OSC/OSC/ErrorEstimator.py
trunk/src/workers/OSC/OSC/ExtremumFinder.py
trunk/src/workers/OSC/OSC/Slicing.py
trunk/src/workers/OSC/OSC/Smoother.py
trunk/src/workers/OSC/OSC/__init__.py
trunk/src/workers/Statistics/Statistics/Histogram.py
trunk/src/workers/fmfile/fmfile/FMFLoader.py
trunk/src/workers/fmfile/fmfile/__init__.py
Modified: trunk/src/pyphant/pyphant/core/DataContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/DataContainer.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/pyphant/pyphant/core/DataContainer.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -31,25 +31,37 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
-DataContainer \t- A Pyphant modul for self-explanatory scientific data
-======================================================================
-\nA Pyphant DataContainer presents the following attributes:
-\t .longname \t- Notation of the data, e.g. 'electric field',
-\t\t\t which is used for the automatic annotation of charts.
-\t .shortname \t- Symbol of the physical variable in LaTeX notation, e.g. 'E_\\alpha',
-\t\t\t which is also used for the automatic annotation of charts.
-\t .id \t\t- Identifier of Enhanced MD5 (emd5) format
-\t\t\t\temd5://NODE/USER/DATETIME/MD5-HASH.TYPESTRING
-\t\t\t which is set by calling method .seal() and
-\t\t\t indicates that the stored information are unchangable.
-\t .label\t- Typical axis description composed from the meta information of the DataContainer.
-\t .data \t- Data object, e.g. numpy.array
+=============================================================================
+**DataContainer** -- A Pyphant module for *self-explanatory scientific data*
+=============================================================================
-DataContainer \t\t- Base class for self-explanatory scientific data
-FieldContainer \t\t- Class describing sampled fields
-SampleContainer \t- Class used for storing realizations of random variables
-generateIndex() \t- Function returning an indexing FieldContainer instance
-parseId()\t\t- Function returning tupple (HASH,TYPESTRING) from given .id attribute.
+The *DataContainer* is Pypahnt's preferred data exchange class. It is
+designed to maximise the interoperability of the various workers
+provided by Pyphant.
+
+It can be seen as an interface for exchanging data between workers and
+visualizers and among workers. It reproduces the self-descriptiveness of the *network
+Common Data Form* (netCDF). Once sealed it is immutable. It can be
+identified by its *emd5* attribute, a unique identifier composed of
+information about the origin of the container.
+
+There are two kinds of DataContainers:
+
+ - L{FieldContainer}
+ - is designed to store *sampled scalar Fields*
+
+ - L{SampleContainer}
+ - is designed to store *tabular data*
+
+
+**SampleConatiner** -- A pyphant module storing tabular data
+=============================================================
+
+The *SampleContainer* combines different FieldContainers that have the
+same numer of sample points to a table-like representation. It stores
+different observations on the same subject per row whereby each column
+comprises a quantity of the same kind. Each row can be regarded as the
+realization of a random variable.
"""
__id__ = "$Id$"
Modified: trunk/src/pyphant/pyphant/core/FieldContainer.py
===================================================================
--- trunk/src/pyphant/pyphant/core/FieldContainer.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/pyphant/pyphant/core/FieldContainer.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,29 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+u"""
+=================================================================
+The **FieldContainer** -- A module storing sampled scalar fields
+=================================================================
+
+The *FieldContainer* represents a class of Pyphant's L{DataContainer}
+module.
+
+ That is Pyphant's module for *self-desriptive scientific data*
+ which is designed to maximise the interoperability of the various
+ workers. It can be seen as an interface for exchanging scientific
+ information between workers and visualizers. It reproduces the
+ self-descriptiveness of the *network Common Data Form* (netCDF). Once
+ sealed a DataContainer is immutable but can be identified by
+ its *emd5* format which holds information about the origin of
+ the container.
+
+The *FieldContainer* stores a sampled scalar Filed.
+
+ It holds an *n-dimensional array* together with
+ its *unit* and coordinates of the idependent variable (*dimensions*).
+"""
+
__id__ = "$Id$"
__author__ = "$Author$"
__version__ = "$Revision$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/ApplyMask.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -29,7 +29,10 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-u"""Class ApplyMask of Pyphant's Imageprocessing toolbox.
+u"""
+The ApplyMask Worker is a class of Pyphant's Image Processing
+Toolbox. By using this worker one gry-scale image can be applied as a
+mask on another image.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/CoverageWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,10 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Coverage Worker is a class of Pyphant's Image Processing
+toolbox. It compares everx pixel with a calculated
+threshold. Therefore required percentages of black and white material
+in the image can be edited.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/DiffWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,9 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Diff Worker belongs to Pyphant's Image Processing Toolbox. It
+computes the difference between two images, eg. the skeletonised image
+and the origial image.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,8 +30,11 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Distance Mapper Worker is a class of Pyphant's Image Processing
+Toolbox. It is used to determine the size of respective features in
+binary images through calculating the distance of every pixel to the
+nearest background pixel.
"""
-
__id__ = "$Id: /local/pyphant/sourceforge/trunk/src/workers/ImageProcessing/ImageProcessing/DistanceMapper.py 3671 2007-12-19T14:18:11.779018Z obi $"
__author__ = "$Author: obi $"
__version__ = "$Revision: 3671 $"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/EdgeFillWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Edge Fill Worker is a class of Pyphant's Image Processing
+Toolbox. It is used to backfil outlined features again.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/EdgeTouchingFeatureRemover.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,9 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Touching Feature Remover Worker is a class of Pyphant's Image Processing
+Toolbox. It removes all features of an image that are touching the
+edge until only the outline remains.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/ImageLoaderWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,9 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The ImageLoader Worker is a class of Pyphant's Image Processing
+Toolbox. It simply loads an image from the location given in the
+worker's configuration.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/InvertWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Inverter Worker is a class of Pyphant's Image Processing
+Toolbox. It simply inverts an image.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/Medianiser.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,10 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Madianiser Worker is a class of Pyphant's Image Processing
+Toolbox. It is used to remove noise from an image, by implementing a
+standard median filter. In its configurations the size of the applied
+kernel and the number of smoothing runs can be edited.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/ThresholdingWorker.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,10 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Thresholding Worker is a class of Pyphant's image Processing
+Toolbox. The threshold can be edited in the worker's configuration. It
+returns a binary image where pixels that comprise features are set to
+0x00 whereas background pixels are set to 0xFF.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/UltimatePointsCalculator.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Ultimate Points Calculator Worker is a class of Pyphant's Image
+Processing Toolbox. It is used to calculate peaks in an image.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,7 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The ImageProcessing toolbox holds workers to process data resulting from scalar fields.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/AddColumn.py
===================================================================
--- trunk/src/workers/OSC/OSC/AddColumn.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/AddColumn.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,9 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Add Column Worker is a class of Pyphant's OSC Toolbox. It inserts a
+column that was once extracted by using the column extractor in the
+orignial chart again.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/CompareFields.py
===================================================================
--- trunk/src/workers/OSC/OSC/CompareFields.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/CompareFields.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,7 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Compare Fields Worker is a class of Pyphant's OSC Toolbox.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/ComputeFunctional.py
===================================================================
--- trunk/src/workers/OSC/OSC/ComputeFunctional.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/ComputeFunctional.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -29,7 +29,8 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-u"""Pyphant module providing worker for finding the local extrema of 1D functions.
+u"""
+Pyphant module providing worker for finding the local extrema of 1D functions.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/ErrorEstimator.py
===================================================================
--- trunk/src/workers/OSC/OSC/ErrorEstimator.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/ErrorEstimator.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -29,6 +29,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Error Estimaotr Worker is a class of Pyphant's OSC-Toolbox. It
+valuates the error caused by noise for every pixel in a field.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/ExtremumFinder.py
===================================================================
--- trunk/src/workers/OSC/OSC/ExtremumFinder.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/ExtremumFinder.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,7 +30,11 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-u"""Pyphant module computing the local extrema of one-dimensional sampled fields. If a two-dimensional field is provided as input, the algorithm loops over the 0th dimension denoting the y-axis, which corresponds to an iteration over the rows of the data matrix.
+u"""
+Pyphant module computing the local extrema of one-dimensional
+sampled fields. If a two-dimensional field is provided as input, the
+algorithm loops over the 0th dimension denoting the y-axis, which
+corresponds to an iteration over the rows of the data matrix.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/Slicing.py
===================================================================
--- trunk/src/workers/OSC/OSC/Slicing.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/Slicing.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Slicing Worker is a class of Pyphant's OSC Toolbox. It cut out one
+part of a field and provides it as a new field to work on.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/Smoother.py
===================================================================
--- trunk/src/workers/OSC/OSC/Smoother.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/Smoother.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Smoother Worker is a class of Pyphant's OSC Toolbox. It is used to
+reduce noise from a field. The numer of smoothing runs can be edited.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/OSC/OSC/__init__.py
===================================================================
--- trunk/src/workers/OSC/OSC/__init__.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/OSC/OSC/__init__.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The OSC Toolbox holds workers for processing data coming from organic
+solar cells.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/Statistics/Statistics/Histogram.py
===================================================================
--- trunk/src/workers/Statistics/Statistics/Histogram.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/Statistics/Statistics/Histogram.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,10 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The Historgam Worker is a class of Pyphant's Statistic Toolbox. It
+calcuates a histogram from the provided data. Histograms can be
+visualisd as bar charts or line charts. The rexpective axes are
+automatically correctly labled.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/fmfile/fmfile/FMFLoader.py
===================================================================
--- trunk/src/workers/fmfile/fmfile/FMFLoader.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/fmfile/fmfile/FMFLoader.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,8 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The FMF Loader is a class of Pyphant's FMF Toolbox. It loads an FMF
+file from the location given in the worker's configuration.
"""
__id__ = "$Id$"
Modified: trunk/src/workers/fmfile/fmfile/__init__.py
===================================================================
--- trunk/src/workers/fmfile/fmfile/__init__.py 2009-03-17 13:42:37 UTC (rev 621)
+++ trunk/src/workers/fmfile/fmfile/__init__.py 2009-03-17 14:26:25 UTC (rev 622)
@@ -30,6 +30,7 @@
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
+The FMF Toolbox holds workers for processing full meta data format files.
"""
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