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[Pyphant-devel] SF.net SVN: pyphant:[695] trunk/src
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From: <zk...@us...> - 2010-07-12 20:43:18
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Revision: 695
http://pyphant.svn.sourceforge.net/pyphant/?rev=695&view=rev
Author: zklaus
Date: 2010-07-12 20:43:11 +0000 (Mon, 12 Jul 2010)
Log Message:
-----------
Merge branch 'master' into svn-trunk
* master:
Enh: Import of single microscopy images
Modified Paths:
--------------
trunk/src/pyphant/pyphant/core/ZStackManager.py
trunk/src/pyphant/pyphant/tests/TestZStacks.py
trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
Added Paths:
-----------
trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
Modified: trunk/src/pyphant/pyphant/core/ZStackManager.py
===================================================================
--- trunk/src/pyphant/pyphant/core/ZStackManager.py 2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/core/ZStackManager.py 2010-07-12 20:43:11 UTC (rev 695)
@@ -39,65 +39,27 @@
# $Source$
-from pyphant.core.XMLHandler import getXMLRoot
from pyphant.quantities import Quantity
from pyphant.core.DataContainer import (FieldContainer, SampleContainer)
import scipy
import Image
from pyphant.core.KnowledgeManager import KnowledgeManager
import os
+import re
kmanager = KnowledgeManager.getInstance()
class ZStack(object):
- def __init__(self, sc_id=None, name=None, xml_file=None, temporary=False):
- """Initializes a ZStack from an existing id or a local source"""
- assert (sc_id is None) is not (xml_file is None)
+ def __init__(self, sc_id=None, meta=None, temporary=False):
+ """Initializes a ZStack from an existing id or metadata"""
+ assert (sc_id is None) is not (meta is None)
self.temporary = temporary
- self._recipe_path = None
if sc_id is not None:
self.repr_sc = kmanager.getDataContainer(sc_id)
else:
- assert name is not None
- self.repr_sc = self._import_zstack(name,
- os.path.realpath(xml_file))
+ self.repr_sc = self._import_zstack(meta)
@staticmethod
- def _get_images_meta(xml_file):
- def getFloat(xmlelement):
- return float(xmlelement.content.strip().replace(',', '.'))
-
- def getMum(xmlelement):
- return Quantity(getFloat(xmlelement), 'mum')
-
- base_path = os.path.dirname(xml_file)
- xml_root = getXMLRoot(xml_file)
- images_meta = []
- for ztag in [value for key, value in xml_root.children.iteritems()\
- if key.startswith('z')]:
- meta = {}
- fname = xml_root['Tags']['V5'].content.strip()
- root, ext = os.path.splitext(fname)
- fname = "%s_%s%s" % (root, ztag.name, ext)
- meta['img_filename'] = os.path.join(base_path, fname)
- meta['zvi_filename'] = os.path.join(
- base_path, xml_root['Tags']['V150'].content.strip())
- meta['xml_filename'] = xml_file
- meta['zid'] = ztag.name
- ztag = ztag['Tags']
- meta['timestamp'] = ztag['V44'].content.strip()
- meta['width'] = int(ztag['V3'].content.strip())
- meta['height'] = int(ztag['V4'].content.strip())
- meta['x-pos'] = getMum(ztag['V15'])
- meta['y-pos'] = getMum(ztag['V16'])
- meta['z-pos'] = getMum(ztag['V93'])
- meta['pixel_width'] = getMum(xml_root['Scaling']['Factor_0'])
- meta['pixel_height'] = getMum(xml_root['Scaling']['Factor_1'])
- images_meta.append(meta)
- images_meta.sort(key = lambda x: x['z-pos'].value)
- return images_meta
-
- @staticmethod
def _get_image_fcs(images_meta, temporary=False):
zvalues = []
emd5s = []
@@ -111,47 +73,43 @@
count = 1
for img_meta in images_meta:
if pdial is not None:
- pdial.Update(count, os.path.basename(img_meta['img_filename']))
+ pdial.Update(count, os.path.basename(img_meta['imgFilename']))
count += 1
- files.append(img_meta['xml_filename'])
- img = Image.open(img_meta['img_filename'])
+ files.append(img_meta['xmlFilename'])
+ img = Image.open(img_meta['imgFilename'])
data = scipy.misc.fromimage(img, flatten=True)
zvalue = img_meta['z-pos']
- ydata = scipy.arange(img_meta['height']) \
- * img_meta['pixel_height'].inUnitsOf('mum').value \
- + img_meta['y-pos'].inUnitsOf('mum').value
- xdata = scipy.arange(img_meta['width']) \
- * img_meta['pixel_width'].inUnitsOf('mum').value \
- + img_meta['x-pos'].inUnitsOf('mum').value
+ yunit = Quantity(1.0, img_meta['height'].unit)
+ xunit = Quantity(1.0, img_meta['width'].unit)
+ ydata = scipy.arange(img_meta['height[pixel]']) \
+ * img_meta['y-factor'].inUnitsOf(yunit.unit).value \
+ + img_meta['y-pos'].inUnitsOf(yunit.unit).value
+ xdata = scipy.arange(img_meta['width[pixel]']) \
+ * img_meta['x-factor'].inUnitsOf(xunit.unit).value \
+ + img_meta['x-pos'].inUnitsOf(xunit.unit).value
dimensions = [FieldContainer(ydata,
- unit=Quantity(1.0, 'mum'),
+ unit=yunit,
longname=u'y-axis',
shortname=u'y'),
FieldContainer(xdata,
- unit=Quantity(1.0, 'mum'),
+ unit=xunit,
longname=u'x-axis',
shortname=u'x')]
- fcattr = {'img_filename':img_meta['img_filename'],
- 'xml_filename':img_meta['xml_filename'],
- 'zvi_filename':img_meta['zvi_filename'],
- 'zvalue':zvalue,
- 'timestamp':img_meta['timestamp'],
- 'zid':img_meta['zid'],
- 'ZStackType':'RawImage',
- 'vmin':0, 'vmax':255}
+ fcattr = {'vmin':0, 'vmax':255}
+ fcattr.update(img_meta)
img_fc = FieldContainer(data=data,
longname=os.path.basename(
- img_meta['img_filename']),
+ img_meta['imgFilename']),
shortname="i",
dimensions=dimensions, attributes=fcattr)
img_fc.seal()
kmanager.registerDataContainer(img_fc, temporary=temporary)
emd5s.append(img_fc.id)
- zvalues.append(zvalue.inUnitsOf('mum').value)
+ zvalues.append(zvalue.value)
if len(zvalues) == 0:
return None, None, None
zfc = FieldContainer(scipy.array(zvalues), longname='z-value',
- shortname='z', unit=Quantity(1.0, 'mum'))
+ shortname='z', unit=Quantity(1.0, zvalue.unit))
filefc = FieldContainer(scipy.array(files), longname='filename',
shortname='f')
emd5fc = FieldContainer(scipy.array(emd5s), longname='emd5',
@@ -160,26 +118,16 @@
pdial.Destroy()
return zfc, filefc, emd5fc
- @staticmethod
- def _estimate_ztol(zfc):
- zmums = [(float(zvalue) * zfc.unit).inUnitsOf('mum').value \
- for zvalue in zfc.data]
- zmums.sort()
- diffs = []
- for index in xrange(len(zmums) - 1):
- diffs.append(zmums[index + 1] - zmums[index])
- return Quantity(2.0 * sum(diffs) / float(len(diffs)), 'mum')
-
- def _import_zstack(self, name, xml_file):
- images_meta = ZStack._get_images_meta(xml_file)
- zfc, filefc, emd5fc = ZStack._get_image_fcs(images_meta, self.temporary)
+ def _import_zstack(self, meta):
+ zfc, filefc, emd5fc = ZStack._get_image_fcs(meta, self.temporary)
if zfc == None:
return None
attributes = {}
- attributes['ztol'] = ZStack._estimate_ztol(zfc)
attributes['ZStackType'] = 'RawSC'
+ attributes['xmlFilename'] = meta[0]['xmlFilename']
+ attributes['crystal'] = meta[0]['crystal']
ssc = SampleContainer([zfc, filefc, emd5fc],
- name,
+ meta[0]['ZStackName'],
"z",
attributes)
ssc.seal()
@@ -188,9 +136,10 @@
class ZStackManager(object):
- def addZStack(self, zstack):
- """Adds a given zstack to the pool"""
- kmanager.registerDataContainer(zstack.repr_sc)
+ def importZStack(self, xmlFName, name, crystal, temporary=False):
+ metaReader = getMetaReader(xmlFName, name, crystal)
+ meta = metaReader.getMeta()
+ return ZStack(meta=meta, temporary=temporary)
def getZStacks(self):
"""Returns a list of all ZStacks in the pool"""
@@ -208,3 +157,141 @@
raise ValueError("There is no ZStack called %s!" \
% name)
return ZStack(sc_id=sresult[0][0])
+
+
+class MetaReader(object):
+ def __init__(self, xmlFName, name, crystal):
+ self.xmlFName = xmlFName
+ from pyphant.core.XMLHandler import getXMLRoot
+ self.xmlRoot = getXMLRoot(xmlFName)
+ self.zStackName = name
+ self.crystal = crystal
+
+ def getMeta(self):
+ getStr = lambda x: x.content.strip()
+ def getTag(tag, tagstr):
+ for subtag in tagstr.split(':'):
+ tag = tag[subtag]
+ return tag
+ common_meta = {}
+ for key, tagstr in self.commonTagDict.iteritems():
+ common_meta[key] = getStr(getTag(self.xmlRoot, tagstr))
+ common_meta['xmlFilename'] = self.xmlFName
+ images_meta = []
+ for ztag in [value for key, value in self.xmlRoot.children.iteritems()\
+ if self.tagRe.match(key) is not None]:
+ meta = common_meta.copy()
+ for key, tagstr in self.imageTagDict.iteritems():
+ meta[key] = getStr(getTag(ztag, tagstr))
+ meta['zid'] = self.getZId(ztag.name)
+ meta['pid'] = self.getPId(ztag.name)
+ meta['imgFilename'] = self.getImgFName(ztag.name)
+ meta['ZStackName'] = self.zStackName
+ meta['crystal'] = self.crystal
+ images_meta.append(meta)
+ self.validateMeta(images_meta)
+ images_meta.sort(key = lambda x: x['z-pos'].value)
+ return images_meta
+
+
+class ZStackMetaReader(MetaReader):
+ commonTagDict = {'scalingfactor 0':'Scaling:Factor_0',
+ 'scalingfactor 1':'Scaling:Factor_1',
+ 'SF type 0':'Scaling:Type_0',
+ 'SF type 1':'Scaling:Type_1',
+ 'width[pixel]':'Tags:V25',
+ 'height[pixel]':'Tags:V26',
+ 'width':'Tags:V30',
+ 'height':'Tags:V33',
+ 'width type':'Tags:V28',
+ 'height type':'Tags:V31',
+ 'x-factor':'Tags:V29',
+ 'y-factor':'Tags:V32',
+ 'x-pos':'Tags:V48',
+ 'y-pos':'Tags:V49',
+ 'objective':'Tags:V101'}
+ imageTagDict = {'timestamp':'Tags:V44',
+ 'z-pos':'Tags:V93'}
+ tagRe = re.compile(r'^z[0-9]+$')
+
+ def getImgFName(self, ztagname):
+ fname = self.xmlRoot['Tags']['V5'].content.strip()
+ root, ext = os.path.splitext(fname)
+ fname = "%s_%s%s" % (root, ztagname, ext)
+ return os.path.join(os.path.dirname(self.xmlFName), fname)
+
+ def getZId(self, ztagname):
+ return int(ztagname[1:])
+
+ def getPId(self, ztagname):
+ return 0
+
+ def validateMeta(self, meta):
+ getFloat = lambda x: float(x.replace(',', '.'))
+ getMum = lambda x: Quantity(getFloat(x), 'mum')
+ mumErr = 'Expected micrometre but got different unit!'
+ for img_meta in meta:
+ assert img_meta.pop('SF type 0') == '76', mumErr
+ assert img_meta.pop('SF type 1') == '76', mumErr
+ assert img_meta.pop('width type') == '76', mumErr
+ assert img_meta.pop('height type') == '76', mumErr
+ assert getFloat(img_meta.pop('scalingfactor 0')) \
+ == getFloat(img_meta['x-factor'])
+ assert getFloat(img_meta.pop('scalingfactor 1')) \
+ == getFloat(img_meta['y-factor'])
+ for key in ['width', 'height', 'x-factor', 'y-factor', 'x-pos',
+ 'y-pos', 'z-pos']:
+ img_meta[key] = getMum(img_meta[key])
+ for key in ['width[pixel]', 'height[pixel]']:
+ img_meta[key] = int(img_meta[key])
+ assert img_meta['width[pixel]'] == int(round(img_meta['width'] /\
+ img_meta['x-factor'])), "x scaling is void"
+ assert img_meta['height[pixel]'] == int(round(img_meta['height'] /\
+ img_meta['y-factor'])), "y scaling is void"
+
+
+class SingleMetaReader(ZStackMetaReader):
+ commonTagDict = {'scalingfactor 0':'Scaling:Factor_0',
+ 'scalingfactor 1':'Scaling:Factor_1',
+ 'SF type 0':'Scaling:Type_0',
+ 'SF type 1':'Scaling:Type_1',
+ 'width[pixel]':'Tags:V11',
+ 'height[pixel]':'Tags:V12',
+ 'width':'Tags:V16',
+ 'height':'Tags:V19',
+ 'width type':'Tags:V14',
+ 'height type':'Tags:V17',
+ 'x-factor':'Tags:V15',
+ 'y-factor':'Tags:V18',
+ 'x-pos':'Tags:V41',
+ 'y-pos':'Tags:V42',
+ 'objective':'Tags:V93',
+ 'timestamp':'Tags:V50',
+ 'z-pos':'Tags:V99'}
+ imageTagDict = {}
+ tagRe = re.compile(r'^_single$')
+
+ def getZId(self, ztagname):
+ return 0
+
+ def getImgFName(self, ztagname):
+ fname = self.xmlRoot['Tags']['V5'].content.strip()
+ return os.path.join(os.path.dirname(self.xmlFName), fname)
+
+META_READERS = [ZStackMetaReader, SingleMetaReader]
+
+def getMetaReader(xml, name, crystal):
+ from pyphant.core.XMLHandler import getXMLRoot
+ root = getXMLRoot(xml)
+ matched = False
+ for key in root.children.iterkeys():
+ for mreader in META_READERS:
+ if mreader.tagRe.match(key) is not None:
+ matched = True
+ break
+ if matched:
+ break
+ if matched:
+ return mreader(xml, name, crystal)
+ else:
+ raise ValueError("Unknown file format in file: %s" % xml)
Modified: trunk/src/pyphant/pyphant/tests/TestZStacks.py
===================================================================
--- trunk/src/pyphant/pyphant/tests/TestZStacks.py 2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/tests/TestZStacks.py 2010-07-12 20:43:11 UTC (rev 695)
@@ -60,12 +60,12 @@
import os
from pyphant.core import KnowledgeManager
from pyphant import __path__ as ppath
- from pyphant.core.ZStackManager import ZStack
+ from pyphant.core.ZStackManager import ZStackManager
print "Importing ZStack..."
- zstack = ZStack(name="TestCase_ZStack",
- xml_file=os.path.join(ppath[0], "tests", "resources",
+ zstack = ZStackManager().importZStack(name="TestCase_ZStack",
+ xmlFName=os.path.join(ppath[0], "tests", "resources",
"zstack", "_meta.xml"),
- temporary=True)
+ temporary=True, crystal='TestCrystal')
print "Done."
print "Calculating ZStack-statistics..."
from ImageProcessing.AutoFocus import AutoFocus
@@ -84,7 +84,25 @@
self.check((300.0, 0.0), statistics['z-pos'].data[imin])
self.check((7.0, 1.0), statistics['diameter'].data[imin])
+ def testSingle(self):
+ import os
+ from pyphant.core import KnowledgeManager
+ from pyphant import __path__ as ppath
+ from pyphant.core.ZStackManager import ZStackManager
+ print "Importing single image..."
+ zstack = ZStackManager().importZStack(name="TestCase_Single",
+ xmlFName=os.path.join(ppath[0], "tests", "resources",
+ "zstack", "single_meta.xml"),
+ temporary=True, crystal='TestCrystal2')
+ print "Done."
+ print "Calculating single image statistics..."
+ from ImageProcessing.AutoFocus import AutoFocus
+ afw = AutoFocus()
+ statistics = afw.get_statistics_sc(zstack.repr_sc)
+ print "Done."
+ assert len(statistics['diameter'].data) == 2
+
if __name__ == "__main__":
import sys
if len(sys.argv) == 1:
Modified: trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml
===================================================================
--- trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml 2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/tests/resources/zstack/_meta.xml 2010-07-12 20:43:11 UTC (rev 695)
@@ -2,11 +2,23 @@
<ROOT>
<Tags>
<V5>TestZStack.tif</V5>
- <V150></V150>
+ <V25>400</V25>
+ <V26>400</V26>
+ <V29>1,0</V29>
+ <V30>400,0</V30>
+ <V28>76</V28>
+ <V32>1,0</V32>
+ <V33>400,0</V33>
+ <V31>76</V31>
+ <V48>0,0</V48>
+ <V49>0,0</V49>
+ <V101>TestObjective</V101>
</Tags>
<Scaling>
<Factor_0>1,00</Factor_0>
<Factor_1>1,00</Factor_1>
+ <Type_0>76</Type_0>
+ <Type_1>76</Type_1>
</Scaling>
<z00>
<Tags>
Added: trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml
===================================================================
--- trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml (rev 0)
+++ trunk/src/pyphant/pyphant/tests/resources/zstack/single_meta.xml 2010-07-12 20:43:11 UTC (rev 695)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<ROOT>
+ <Tags>
+ <V5>TestZStack_z04.tif</V5>
+ <V11>400</V11>
+ <V12>400</V12>
+ <V15>1,0</V15>
+ <V16>400,0</V16>
+ <V14>76</V14>
+ <V18>1,0</V18>
+ <V19>400,0</V19>
+ <V17>76</V17>
+ <V41>0,0</V41>
+ <V42>0,0</V42>
+ <V93>TestObjective</V93>
+ <V50>12.07.2010 09:40:00</V50>
+ <V99>0,0</V99>
+ </Tags>
+ <Scaling>
+ <Factor_0>1,00</Factor_0>
+ <Factor_1>1,00</Factor_1>
+ <Type_0>76</Type_0>
+ <Type_1>76</Type_1>
+ </Scaling>
+ <_single>
+ <Tags>
+ </Tags>
+ </_single>
+</ROOT>
Modified: trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py
===================================================================
--- trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py 2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/pyphant/pyphant/wxgui2/wxPyphantApplication.py 2010-07-12 20:43:11 UTC (rev 695)
@@ -480,7 +480,7 @@
defaultFile="", wildcard=wc, style=wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename = os.path.realpath(dlg.GetPath())
- from pyphant.core.ZStackManager import (ZStack, ZStackManager)
+ from pyphant.core.ZStackManager import ZStackManager
tedlg = wx.TextEntryDialog(self, "Enter name for ZStack:",
"", "ZStack")
if tedlg.ShowModal() == wx.ID_OK:
@@ -491,10 +491,15 @@
cpt2 = "Error"
msg2 = "ZStack %s already exists!" % name
except ValueError:
- zstack = ZStack(name=name, xml_file=filename)
- zsm.addZStack(zstack)
- cpt2 = "Info"
- msg2 = "Successfully imported ZStack."
+ tedlg2 = wx.TextEntryDialog(self, "Enter crystal name:",
+ "", "Crystal01")
+ if tedlg2.ShowModal() == wx.ID_OK:
+ crystal = tedlg2.GetValue()
+ zsm.importZStack(name=name, xmlFName=filename,
+ crystal=crystal)
+ cpt2 = "Info"
+ msg2 = "Successfully imported ZStack."
+ tedlg2.Destroy()
dlg2 = wx.MessageDialog(self, msg2, cpt2, wx.OK)
dlg2.ShowModal()
dlg2.Destroy()
Modified: trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py
===================================================================
--- trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py 2010-07-08 13:13:29 UTC (rev 694)
+++ trunk/src/workers/ImageProcessing/ImageProcessing/MarkAF.py 2010-07-12 20:43:11 UTC (rev 695)
@@ -106,7 +106,7 @@
output_img = deepcopy(image)
if vmin is not None:
output_img.attributes.update({'vmin':vmin, 'vmax':vmax})
- mf_z = int(image.attributes['zid'][-2:])
+ mf_z = image.attributes['zid']
slicess = [(slice(yt, yp), slice(xt, xp)) \
for yt, yp, xt, xp, z in zip(
statistics['yt'].data, statistics['yp'].data,
@@ -125,7 +125,7 @@
output_img = deepcopy(image)
output_img.data = numpy.zeros(image.data.shape,
dtype=image.data.dtype)
- mf_z = int(image.attributes['zid'][-2:])
+ mf_z = image.attributes['zid']
labelslicess = [(label, (slice(yt, yp), slice(xt, xp))) \
for label, yt, yp, xt, xp, z in zip(
statistics['label'].data,
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