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[Pyphant-devel] SF.net SVN: pyphant:[653] trunk/src
|
From: <zk...@us...> - 2009-07-21 13:41:35
|
Revision: 653
http://pyphant.svn.sourceforge.net/pyphant/?rev=653&view=rev
Author: zklaus
Date: 2009-07-21 13:41:23 +0000 (Tue, 21 Jul 2009)
Log Message:
-----------
Merge branch 'master' into svn-trunk
* master: (37 commits)
Fix: Separated gradient filter from NDImageWorker
Fix: Moved GSInverter to NDImage worker
Fix: Fixed unit of EnhanceContrast worker
Fix: Removed unused parameter from FindLocalExtrema worker
Cosm: Renamed variables in NDImageWorker
Fix: Removed Gradient worker
Fix: Removed broken filters from NDImage worker
Cosm: Changed longnames of output FCs of several workers
Fix: Removed registration of recipes in wxPyphant
Enh: Added MeasureFocus worker
Enh: Changed method for finding extrema
Cosm: Removed commentary in NDImage worker
Enh: Added parameter 'tolerance' to FindLocalExtrema Worker
Enh: Added workers FindLocalExtrema and Watershed (both preliminary)
Enh: Added new filters to NDImage worker
Enh: Added new filters to NDImage worker
Fix: EnhanceContrast worker returns proper types now
Fix: Fixed bug in FitBackground worker
Enh: Added some filters to NDImage worker
Fix: EnhanceContrast worker uses linear stretching now
...
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/H5FileHandler.py
trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
Added Paths:
-----------
trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py
trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py
trunk/src/workers/ImageProcessing/ImageProcessing/MeasureFocus.py
trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
Modified: trunk/src/pyphant/pyphant/core/H5FileHandler.py
===================================================================
--- trunk/src/pyphant/pyphant/core/H5FileHandler.py 2009-07-21 11:42:02 UTC (rev 652)
+++ trunk/src/pyphant/pyphant/core/H5FileHandler.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -37,7 +37,7 @@
__version__ = "$Revision$"
# $Source$:
import tables
-from pyphant.core import DataContainer
+from pyphant.core import (DataContainer, FieldContainer)
from tables import StringCol
from pyphant.quantities.PhysicalQuantities import PhysicalQuantity
import scipy
@@ -143,7 +143,7 @@
+ DataContainer.parseId(row['id'])[0]))
for row in dimTable.iterrows()]
except tables.NoSuchNodeError:
- dimensions = DataContainer.INDEX
+ dimensions = FieldContainer.INDEX
result = DataContainer.FieldContainer(data, unit, error, mask,
dimensions, longname, shortname,
attributes)
@@ -343,7 +343,7 @@
(u"Mask of "+result.longname).encode("utf-8"))
self.handle.setNodeAttr(resultGroup, "unit",
repr(result.unit).encode("utf-8"))
- if result.dimensions != DataContainer.INDEX:
+ if result.dimensions != FieldContainer.INDEX:
idLen = max([len(dim.id.encode("utf-8"))
for dim in result.dimensions])
dimTable = self.handle.createTable(resultGroup, "dimensions",
Modified: trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py 2009-07-21 11:42:02 UTC (rev 652)
+++ trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -181,10 +181,10 @@
if self._wxPyphantApp.pathToRecipe[-3:] == '.h5':
if os.path.exists(self._wxPyphantApp.pathToRecipe):
recipe = pyphant.core.PyTablesPersister.loadRecipeFromHDF5File(self._wxPyphantApp.pathToRecipe)
- from pyphant.core import KnowledgeManager
- KnowledgeManager.KnowledgeManager.getInstance().registerURL(
- "file:///"+os.path.realpath(self._wxPyphantApp.pathToRecipe)
- )
+ #from pyphant.core import KnowledgeManager
+ #KnowledgeManager.KnowledgeManager.getInstance().registerURL(
+ # "file:///"+os.path.realpath(self._wxPyphantApp.pathToRecipe)
+ # )
self._remainingSpace=PyphantCanvas.PyphantCanvas(self, recipe)
else:
self._remainingSpace=PyphantCanvas.PyphantCanvas(self)
Copied: trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py (from rev 652, trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py)
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/EnhanceContrast.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# 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 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__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+
+import ImageProcessing
+from ImageProcessing.NDImageWorker import pile
+import scipy, copy
+
+def normalizeHistogram(data):
+ histogram = scipy.ndimage.histogram(data.astype("f"), 0, 255, 256)
+ cumulatedHistogram = scipy.cumsum(histogram)
+ nch = cumulatedHistogram.astype("f")/len(data.flat)
+ inch = (nch*255).astype("i")
+ normalize = scipy.vectorize(lambda i: inch[i])
+ return normalize(data)
+ #return data
+
+def normalizeLinear(data):
+ res = data - data.min()
+ res = (res * 255) / res.max()
+ return res
+
+class EnhanceContrast(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "EnhanceContrast"
+ _sockets = [("image", Connectors.TYPE_IMAGE)]
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def enhance(self, image, subscriber=0):
+ newdata = pile(normalizeLinear, image.data)
+ longname = "Normalize"
+ result = DataContainer.FieldContainer(
+ newdata,
+ 1,
+ None,
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ #print newdata.shape
+ return result
Added: trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/FindLocalExtrema.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,123 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+
+import ImageProcessing
+from ImageProcessing.NDImageWorker import pile
+import scipy, copy
+from scipy import ndimage
+from numpy import (alltrue, zeros)
+
+class FindLocalExtrema(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "FindLocalExtrema"
+ _sockets = [("image", Connectors.TYPE_IMAGE)]
+ _params = [("maxmin", "max/min", ["max", "min"], None),
+ ("excolor", "marker color (-1 for labeling)", 255, None),
+ ("tolerance", "tolerance in %", 20, None)]
+
+ def compare(self, pvalue, nhood, viewextr):
+ if self.paramMaxmin.value == "max":
+ c = pvalue >= (viewextr * (100 - self.paramTolerance.value)) / 100
+ else:
+ c = pvalue <= (viewextr * (100 + self.paramTolerance.value)) / 100
+ return c
+
+ def getPoints(self, data, sl):
+ if sl[0].stop - sl[0].start < 3 or sl[1].stop - sl[1].start < 3:
+ return []
+ points = []
+ if self.paramMaxmin.value == "max":
+ viewextr = data[sl].max()
+ else:
+ viewextr = data[sl].min()
+ for y in xrange(sl[0].start, sl[0].stop):
+ ydiff = 1
+ if y == 0:
+ ydiff = 0
+ for x in xrange(sl[1].start, sl[1].stop):
+ xdiff = 1
+ if x == 0:
+ xdiff = 0
+ nhood = data[y - ydiff:y + 2,
+ x - xdiff:x + 2]
+ pvalue = data[y, x]
+ if not alltrue(pvalue == nhood):
+ if self.compare(pvalue, nhood, viewextr):
+ if self.paramExcolor.value == -1:
+ color = self.nextlabel
+ else:
+ color = self.paramExcolor.value
+ points.append(((y, x), color))
+ self.nextlabel += 1
+ return points
+
+ def findExtrema(self, data):
+ labeled = ndimage.label(data)[0]
+ self.nextlabel = 1
+ slices = ndimage.find_objects(labeled)
+ res = zeros(data.shape, int)
+ for sl in slices:
+ points = self.getPoints(data, sl)
+ for p, c in points:
+ res[p] = c
+ return res
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def find(self, image, subscriber=0):
+ newdata = pile(self.findExtrema, image.data)
+ longname = "FindLocalExtrema"
+ result = DataContainer.FieldContainer(
+ newdata,
+ copy.deepcopy(image.unit),
+ copy.deepcopy(image.error),
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ #print newdata.shape
+ return result
Added: trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/FitBackground.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,143 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+import ImageProcessing
+import numpy, copy
+from scipy import (ndimage, interpolate)
+
+class FitBackground(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "FitBackground"
+ _sockets = [("image", Connectors.TYPE_IMAGE)]
+ _params = [("poldegree", "Polynomial degree (1 to 5)", 3, None),
+ ("swidth", "sample width", 150, None),
+ ("sheight", "sample height", 150, None),
+ ("threshold", "Background threshold", 255, None),
+ ("mediansize", "Median kernel size", 3, None),
+ ("medianruns", "Median runs", 3, None),
+ ("darksize", "Erosion kernel size", 3, None),
+ ("darkruns", "Erosion runs", 4, None),
+ ("brightsize", "Inverted erosion size", 6, None),
+ ("brightruns", "Inverted erosion runs", 10, None),
+ ("dopreview", "Preview fit input", False, None)]
+
+ def fit(self, data, poldegree, swidth, sheight, threshold):
+ if int(threshold) == -1:
+ threshold = (int(data.mean()) * 10) / 7
+ dims = data.shape
+ xList = []
+ yList = []
+ zList = []
+ for y in xrange(0, dims[0] - 1, sheight):
+ for x in xrange(0, dims[1] - 1, swidth):
+ view = data[y:y + sheight, x:x + swidth]
+ flatIndex = numpy.argmax(view)
+ yIdx, xIdx = numpy.unravel_index(flatIndex, view.shape)
+ zValue = view[yIdx, xIdx]
+ if zValue <= threshold:
+ xList.append(x + xIdx)
+ yList.append(y + yIdx)
+ zList.append(zValue)
+ if len(xList) < (poldegree + 1) * (poldegree + 1):
+ raise ValueError("Not enough reference points.")
+ tck = interpolate.bisplrep(yList, xList, zList,
+ kx=poldegree, ky=poldegree,
+ xb=0, yb=0,
+ xe=int(dims[0]), ye=int(dims[1]))
+ clipmin, clipmax = data.min(), threshold
+ return interpolate.bisplev(range(dims[0]), range(dims[1]),
+ tck).clip(clipmin, clipmax)
+
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def fit_background(self, image, subscriber=0):
+ poldegree = self.paramPoldegree.value
+ swidth = self.paramSwidth.value
+ sheight = self.paramSheight.value
+ threshold = self.paramThreshold.value
+ mediansize = self.paramMediansize.value
+ medianruns = self.paramMedianruns.value
+ darksize = self.paramDarksize.value
+ darkruns = self.paramDarkruns.value
+ brightsize = self.paramBrightsize.value
+ brightruns = self.paramBrightruns.value
+ dopreview = self.paramDopreview.value
+ assert image.data.ndim in [2, 3]
+ if image.data.ndim == 2:
+ pile = [image.data]
+ else:
+ pile = image.data
+ #Median
+ for run in xrange(medianruns):
+ pile = [ndimage.median_filter(data,
+ size=mediansize) for data in pile]
+ #Suspend dark spots:
+ for run in xrange(darkruns):
+ pile = [255 - ndimage.grey_erosion(255 - data,
+ size=darksize) for data in pile]
+ #Suspend features:
+ for run in xrange(brightruns):
+ pile = [ndimage.grey_erosion(data,
+ size=brightsize) for data in pile]
+ #Fit background:
+ if not dopreview:
+ pile = [self.fit(data, poldegree, swidth, sheight,
+ threshold) for data in pile]
+ if image.data.ndim == 2:
+ newdata = pile[0]
+ else:
+ newdata = numpy.array(pile)
+ longname = "FitBackground"
+ result = DataContainer.FieldContainer(
+ newdata,
+ copy.deepcopy(image.unit),
+ copy.deepcopy(image.error),
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ return result
Copied: trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py (from rev 652, trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py)
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/Gradient.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,77 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+import ImageProcessing
+import numpy, copy
+from ImageProcessing.NDImageWorker import pile
+
+def gradient(data):
+ res = numpy.sqrt(sum(
+ numpy.square(numpy.array(numpy.gradient(data)))
+ ))
+ return (res * 255.0).astype(int) / 361
+
+
+class Gradient(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Gradient"
+ _sockets = [("image", Connectors.TYPE_IMAGE)]
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def gradientWorker(self, image, subscriber=0):
+ #TODO: Check whether all dimensions have same unit
+ newdata = gradient(image.data)
+ longname = "Gradient"
+ result = DataContainer.FieldContainer(
+ newdata,
+ (361.0 / 255.0) * (image.unit / image.dimensions[0].unit),
+ None,
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ return result
Added: trunk/src/workers/ImageProcessing/ImageProcessing/MeasureFocus.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/MeasureFocus.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/MeasureFocus.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,95 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+import ImageProcessing
+import numpy, copy
+from scipy import ndimage
+from ImageProcessing.NDImageWorker import pile
+
+class MeasureFocus(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "MeasureFocus"
+ _sockets = [("image", Connectors.TYPE_IMAGE),
+ ("labels", Connectors.TYPE_IMAGE)]
+ _params = [("grow", "grow slices by #n pixels:", 3, None)]
+
+ def getFocus(self, data):
+ #return numpy.sum(numpy.sqrt(numpy.sum(numpy.square(
+ # numpy.array(numpy.gradient(data)))))) / data.size
+ return numpy.sum(data) / data.size
+
+ def sliceAndMeasure(self, data):
+ grow = self.paramGrow.value
+ slices = ndimage.find_objects(self._labels)
+ res = numpy.zeros(data.shape)
+ label = 0
+ for sl in slices:
+ label += 1
+ if sl[0].stop - sl[0].start >= 3 and sl[1].stop - sl[1].start >= 3:
+ start = [sl[0].start - grow, sl[1].start - grow]
+ stop = [sl[0].stop + grow, sl[1].stop + grow]
+ if start[0] < 0: start[0] = 0
+ if start[1] < 0: start[1] = 0
+ bigsl = (slice(start[0], stop[0]), slice(start[1], stop[1]))
+ focus = self.getFocus(data[bigsl])
+ res[sl] = numpy.where(self._labels[sl] == label, focus, res[sl])
+ return res
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def measure_focus(self, image, labels, subscriber=0):
+ self._labels = labels.data
+ newdata = pile(self.sliceAndMeasure, image.data)
+ longname = "MeasureFocus"
+ result = DataContainer.FieldContainer(
+ newdata,
+ copy.deepcopy(image.unit),
+ copy.deepcopy(image.error),
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ return result
Added: trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/NDImageWorker.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,147 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+import ImageProcessing
+import numpy, copy
+from scipy import ndimage
+
+def pile(func, imagedata, runs=1, dopile=True):
+ assert imagedata.ndim in [2, 3]
+ assert runs >= 0
+ if runs == 0:
+ return imagedata
+ if imagedata.ndim == 2 or not dopile:
+ pile = [imagedata]
+ else:
+ pile = imagedata
+ for run in xrange(runs):
+ pile = [func(data) for data in pile]
+ if imagedata.ndim == 2 or not dopile:
+ newdata = pile[0]
+ else:
+ newdata = numpy.array(pile)
+ return newdata
+
+
+class NDImage(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "ndimage"
+ _sockets = [("image", Connectors.TYPE_IMAGE)]
+ _filters = {"binary_closing":("iterations", ),
+ "binary_opening":("iterations", ),
+ "binary_fill_holes":(),
+ "binary_erosion":("iterations", ),
+ "binary_dilation":("iterations", ),
+ "maximum_filter":("size", "mode", "cval"),
+ "median_filter":("size", "mode", "cval"),
+ "grey_closing":("size", "mode", "cval"),
+ "grey_erosion":("size", "mode", "cval"),
+ "grey_opening":("size", "mode", "cval"),
+ "grey_invert":(None, ),
+ "cut_histogram":(None, "tolerance"),
+ "label":(None, "connectivity")}
+ _ndparams = {"iterations":1,
+ "size":5,
+ "mode":["reflect",
+ "nearest",
+ "wrap",
+ "constant"],
+ "cval":0,
+ "tolerance":1000,
+ "connectivity":2}
+ _params = [("pile", "Treat 3d images as pile of 2d images", True, None),
+ ("ndfilter", "Filter", _filters.keys(), None)]
+ _params += [(pn, pn, dflt, None) for pn, dflt in _ndparams.iteritems()]
+
+ def grey_invert(self, data):
+ return 255 - data
+
+ def label(self, data, connectivity):
+ structure = ndimage.morphology.generate_binary_structure(data.ndim,
+ connectivity)
+ return ndimage.label(data, structure=structure)[0]
+
+ def cut_histogram(self, data, tolerance):
+ hist = ndimage.histogram(data, 0, 256, 256)
+ csum = numpy.cumsum(hist)
+ cut = csum[255] / tolerance
+ for i in xrange(len(csum)):
+ if csum[i] > cut:
+ newmin = i
+ break
+ meanvalue = data.mean()
+ return numpy.where(data < newmin, meanvalue, data)
+
+ def applyfilter(self, data):
+ if None in self._filters[self.paramNdfilter.value]:
+ call = getattr(self, self.paramNdfilter.value)
+ else:
+ call = getattr(ndimage, self.paramNdfilter.value)
+ args = {}
+ for par in self._filters[self.paramNdfilter.value]:
+ if par != None:
+ args[par] = self.getParam(par).value
+ print args
+ return call(data, **args)
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def ndimage(self, image, subscriber=0):
+ if "iterations" in self._filters[self.paramNdfilter.value]:
+ runs = 1
+ else:
+ runs = self.paramIterations.value
+ newdata = pile(self.applyfilter, image.data, runs, self.paramPile.value)
+ longname = "%s" % (self.paramNdfilter.value, )
+ result = DataContainer.FieldContainer(
+ newdata,
+ copy.deepcopy(image.unit),
+ None,
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ return result
Added: trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py (rev 0)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/Watershed.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -0,0 +1,110 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2006-2007, Rectorate of the University of Freiburg
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of the Freiburg Materials Research Center,
+# University of Freiburg nor the names of its contributors may be used to
+# endorse or promote products derived from this software without specific
+# prior written permission.
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+u"""
+TODO
+"""
+
+__id__ = "$Id$"
+__author__ = "$Author$"
+__version__ = "$Revision$"
+# $Source$
+
+from pyphant.core import Worker, Connectors,\
+ Param, DataContainer
+
+import ImageProcessing
+from ImageProcessing.NDImageWorker import pile
+import copy
+import heapq, scipy, scipy.ndimage, pylab, threading
+
+class Watershed(Worker.Worker):
+ API = 2
+ VERSION = 1
+ REVISION = "$Revision$"[11:-1]
+ name = "Watershed"
+ _sockets = [("image", Connectors.TYPE_IMAGE),
+ ("markers", Connectors.TYPE_IMAGE)]
+ #_params = [("maxmin", "max/min", ["max", "min"], None),
+ # ("domn", "dominates neighbours by", 0, None)]
+
+ def watershed(self, a):
+ m = self._markers
+ d = scipy.ndimage.distance_transform_edt(a)
+ q = []
+ w = m.copy()
+ for y, x in scipy.argwhere(m!=0):
+ heapq.heappush(q, (-d[y-1, x-1], (y-1, x-1)))
+ heapq.heappush(q, (-d[y-1, x], (y-1, x)))
+ heapq.heappush(q, (-d[y-1, x+1], (y-1, x+1)))
+ heapq.heappush(q, (-d[y, x-1], (y, x-1)))
+ heapq.heappush(q, (-d[y, x+1], (y, x+1)))
+ heapq.heappush(q, (-d[y+1, x-1], (y+1, x-1)))
+ heapq.heappush(q, (-d[y+1, x], (y+1, x)))
+ heapq.heappush(q, (-d[y+1, x+1], (y+1, x+1)))
+ while q:
+ y, x = heapq.heappop(q)[1]
+ l = scipy.unique(w[y-1:y+2,x-1:x+2])
+ l = l[l!=0]
+ if len(l)==1:
+ w[y, x] = l[0]
+ for ny, nx in scipy.argwhere(w[y-1:y+2,x-1:x+2]==0):
+ if (ny==1) and (nx==1):
+ continue
+ ny += y - 1
+ nx += x - 1
+ try:
+ p = (-d[ny,nx], (ny, nx))
+ d[ny,nx] = 0
+ if p[0]!=0 and not p in q:
+ heapq.heappush(q, p)
+ except IndexError, e:
+ print e
+ return w
+
+ @Worker.plug(Connectors.TYPE_IMAGE)
+ def wsworker(self, image, markers, subscriber=0):
+ self._markers = markers.data
+ newdata = pile(self.watershed, image.data)
+ longname = "Watershed"
+ result = DataContainer.FieldContainer(
+ newdata,
+ copy.deepcopy(image.unit),
+ copy.deepcopy(image.error),
+ copy.deepcopy(image.mask),
+ copy.deepcopy(image.dimensions),
+ longname,
+ image.shortname,
+ copy.deepcopy(image.attributes),
+ False)
+ result.seal()
+ #print newdata.shape
+ return result
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py 2009-07-21 11:42:02 UTC (rev 652)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/__init__.py 2009-07-21 13:41:23 UTC (rev 653)
@@ -48,13 +48,20 @@
"DistanceMapper",
"EdgeFillWorker",
"EdgeTouchingFeatureRemover",
+ "EnhanceContrast",
"FilterWorker",
+ "FindLocalExtrema",
+ "FitBackground",
+ "Gradient",
"ImageLoaderWorker",
"InvertWorker",
"Medianiser",
+ "MeasureFocus",
+ "NDImageWorker",
"SkeletonizeFeature",
"ThresholdingWorker",
"UltimatePointsCalculator",
+ "Watershed"
]
def isFeature(point):
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