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Changeset 93

Timestamp:

09/19/07 13:52:48 (11 months ago)

Author:

andrew

Message:

Applied Version 2 - September 2007 changes to schema and improved Tiff chacks in validator

Location:

Files:

: 2 added
: 9 modified

Validator/Backend/OmeValidator.py (modified) (3 diffs)
Validator/Backend/RunAndCheck.py (modified) (2 diffs)
Validator/Backend/ValidatorBackend.tmproj (modified) (5 diffs)
Validator/Backend/mateTiff.py (added)
Validator/Backend/ome-fc-tiff.xsd (modified) (1 diff)
Validator/WebApp/validator/OmeValidator.py (modified) (12 diffs)
Working (modified) (1 prop)
Working/AnalysisModule.xsd (modified) (1 diff)
Working/SPW.xsd (modified) (6 diffs)
Working/completesample-local.xml (added)
Working/ome.xsd (modified) (8 diffs)

Legend:

: Unmodified
: Added
: Removed

Xml/Validator/Backend/OmeValidator.py

r92	r93
238	238	# create an IO string for the xml string provided
239	239	stringXml = StringIO(self.theDom.toxml())
	240
	241	#
	242	print self.theDom.toprettyxml()
	243
240	244	# building the document tree from the input xml
241	245	try:
…	…
440	444	pass
441	445
	446	self.isOmeTiffConsistent = True
	447
442	448	# compare with values from xml and tiff
443	449	if self.tiffFileFrames > self.ome5dPlaneCount:
…	…
454	460	if self.tiffFileFrames < totalTiffDataFrames:
455	461	self.errorList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s out of %s" % (self.tiffFileFrames,totalTiffDataFrames)) , "Not all required frames are present in this Tiff file"))
456
	462	self.isOmeTiffConsistent = False
	463
457	464	# Used by sax parser to handle errors when processing Elements
458	465	class ParseErrorHandler(sax.ErrorHandler):

Xml/Validator/Backend/RunAndCheck.py

r86	r93
15	15
16	16	def main():
	17	print OmeValidator.XmlReport.validateTiff("samples/claire-multi-channel-4D-series.ome.tif")
	18	"""
17	19	for aFilename in ["samples/completesamplenopre.xml","samples/completesample.xml",
18	20	"samples/sdub.ome", "samples/sdub-fix.ome", "samples/sdub-fix-pre.ome",
…	…
26	28	print "============ XML file %s ============ " % aFilename
27	29	print OmeValidator.XmlReport.validateTiff(aFilename)
28
	30	"""
29	31	print "============"
30	32

Xml/Validator/Backend/ValidatorBackend.tmproj

r92	r93
4	4	<dict>
5	5	<key>currentDocument</key>
6		<string>~~OmeValidator~~.py</string>
	6	<string>RunAndCheck.py</string>
7	7	<key>documents</key>
8	8	<array>
9	9	<dict>
10	10	<key>filename</key>
	11	<string>mateTiff.py</string>
	12	<key>lastUsed</key>
	13	<date>2007-09-17T09:26:23Z</date>
	14	</dict>
	15	<dict>
	16	<key>filename</key>
11	17	<string>RunAndCheck.py</string>
12	18	<key>lastUsed</key>
13		<date>2007-09-06T11:24:18Z</date>
	19	<date>2007-09-18T09:26:59Z</date>
	20	<key>selected</key>
	21	<true/>
14	22	</dict>
15	23	<dict>
…	…
17	25	<string>OmeValidator.py</string>
18	26	<key>lastUsed</key>
19		<date>2007-09-13T09:19:26Z</date>
20		<key>selected</key>
21		<true/>
	27	<date>2007-09-18T09:26:59Z</date>
22	28	</dict>
23	29	<dict>
…	…
53	59	<dict>
54	60	<key>column</key>
55		<integer>21</integer>
	61	<integer>8</integer>
56	62	<key>line</key>
57		<integer>35</integer>
	63	<integer>241</integer>
	64	</dict>
	65	<key>firstVisibleColumn</key>
	66	<integer>0</integer>
	67	<key>firstVisibleLine</key>
	68	<integer>206</integer>
	69	</dict>
	70	<key>RunAndCheck.py</key>
	71	<dict>
	72	<key>caret</key>
	73	<dict>
	74	<key>column</key>
	75	<integer>1</integer>
	76	<key>line</key>
	77	<integer>29</integer>
58	78	</dict>
59	79	<key>firstVisibleColumn</key>
…	…
61	81	<key>firstVisibleLine</key>
62	82	<integer>0</integer>
	83	</dict>
	84	<key>mateTiff.py</key>
	85	<dict>
	86	<key>caret</key>
	87	<dict>
	88	<key>column</key>
	89	<integer>0</integer>
	90	<key>line</key>
	91	<integer>24</integer>
	92	</dict>
	93	<key>firstVisibleColumn</key>
	94	<integer>0</integer>
	95	<key>firstVisibleLine</key>
	96	<integer>19</integer>
63	97	</dict>
64	98	<key>samples/completesamplenoenc.xml</key>
…	…
137	171	<key>openDocuments</key>
138	172	<array>
	173	<string>mateTiff.py</string>
139	174	<string>OmeValidator.py</string>
	175	<string>RunAndCheck.py</string>
140	176	</array>
141	177	<key>showFileHierarchyDrawer</key>
142	178	<true/>
143	179	<key>windowFrame</key>
144		<string>{{~~162, 48}, {1189, 83~~0}}</string>
	180	<string>{{580, 61}, {788, 840}}</string>
145	181	</dict>
146	182	</plist>

Xml/Validator/Backend/ome-fc-tiff.xsd

r75	r93
8	8	xmlns:Bin = "http://www.openmicroscopy.org/XMLschemas/BinaryFile/RC1/BinaryFile.xsd"
9	9	xmlns:CA = "http://www.openmicroscopy.org/XMLschemas/CA/RC1/CA.xsd"
10		version = "FC"
	10	version = "FC+TIFF"
11	11	elementFormDefault = "qualified">
12	12	<xs:import namespace = "http://www.openmicroscopy.org/XMLschemas/AnalysisModule/RC1/AnalysisModule.xsd" schemaLocation = "http://www.openmicroscopy.org/XMLschemas/AnalysisModule/RC1/AnalysisModule.xsd"/>

Xml/Validator/WebApp/validator/OmeValidator.py

r88	r93
18	18
19	19	# Standard Imports
20		import logging~~, cherrypy~~
	20	import logging
21	21	from xml.dom.minidom import getDOMImplementation
22	22	from StringIO import StringIO
…	…
25	25	from stat import *
26	26
27		# LocalDir for shames
	27
	28	# Load schemas from configured directory
	29	import cherrypy
	30	# LocalDir for schemas
28	31	SCHEMA_DIR = cherrypy.config.get("validator.schema", os.path.join(os.getcwd(),"schema"))
29
	32	def schemaFilePath(inFilename):
	33	return os.path.join(os.getcwd(), SCHEMA_DIR, inFilename)
	34	"""
	35	# Load schemas from current directory
	36	def schemaFilePath(inFilename):
	37	return inFilename
	38	"""
30	39	# Try to load Image for XML Schema Vlaidation Support
31	40	haveTiffSupport = True
…	…
135	144	warningList = None
136	145	unresolvedList = None
	146
	147	"""
	148	Create variables used to check internal consistency
	149	"""
	150	# count of TiffData elements founf in the XML
	151	omeTiffDataCount = None
	152	# count of image frames found in Tiff file
	153	tiffFileFrames = None
	154
	155	# count of pixels
	156	omePixelsCount = None
	157	# count of planes
	158	omePlanesCount = None
	159	# count of Z * C * T
	160	ome5dPlaneCount = None
	161	# count of number of times a tiff data block has asked for "all available frames" - value of more then 1 indicates an error
	162	theAllFrameCount = None
137	163
138	164	def __init__(self):
…	…
212	238	# create an IO string for the xml string provided
213	239	stringXml = StringIO(self.theDom.toxml())
	240
	241	#
	242	# print self.theDom.toprettyxml()
	243
214	244	# building the document tree from the input xml
215	245	try:
…	…
232	262	# choose the schema source
233	263	# assume the new schema
234		theSchemaFile = ~~os.path.join(os.getcwd(), SCHEMA_DIR, "ome-2007-07.xsd")~~
	264	theSchemaFile = "ome-2007-07.xsd"
235	265	# if old schema
236	266	if self.theNamespace == "http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd":
…	…
238	268	if self.isOmeTiff:
239	269	# use special tiff version of old schema
240		theSchemaFile = ~~os.path.join(os.getcwd(), SCHEMA_DIR, "ome-fc-tiff.xsd")~~
	270	theSchemaFile = "ome-fc-tiff.xsd"
241	271	else:
242	272	# use normal version of old schema
243		theSchemaFile = ~~os.path.join(os.getcwd(), SCHEMA_DIR, "ome-fc.xsd")~~
	273	theSchemaFile = "ome-fc.xsd"
244	274
245	275	# loading the OME schema to validate against
246	276	try:
247		schema = etree.XMLSchema(etree.parse(~~theSchemaFile~~))
	277	schema = etree.XMLSchema(etree.parse(schemaFilePath(theSchemaFile)))
248	278	except:
249	279	#chosen scema failed to laod
…	…
275	305	if reference not in handlerContent.ids:
276	306	self.unresolvedList.append(ParseMessage(None, None, None, "UnresolvedID",None, reference))
	307
	308	# store the internal counters
	309	self.omeTiffDataCount = handlerContent.omeTiffDataCount
	310	self.omePixelsCount = handlerContent.omePixelsCount
	311	self.omePlanesCount = handlerContent.omePlanesCount
	312	self.ome5dPlaneCount = handlerContent.ome5dPlaneCount
	313	self.omeTiffDataPlaneCount = handlerContent.omeTiffDataPlaneCount
	314	self.theAllFrameCount = handlerContent.theAllFrameCount
277	315
278	316	# store the namespace
…	…
358	396	# parse the new string/file object into the report and validate it
359	397	theTiffReport.parse(theFileString)
	398	theTiffReport.validateTiffImageData(image)
	399	"""
	400	# print theXml
	401	print "Tiff Frames : %s" % theTiffReport.tiffFileFrames
	402	print "Ome Frames : %s" % theTiffReport.omeTiffDataCount
	403	print "Ome Pixels : %s" % theTiffReport.omePixelsCount
	404	print "Ome Planes : %s" % theTiffReport.omePlanesCount
	405	print "Ome 5dPlane : %s" % theTiffReport.ome5dPlaneCount
	406	print "Ome TiffPlane : %s" % theTiffReport.omeTiffDataPlaneCount
	407	print "Ome AllFrame : %s" % theTiffReport.theAllFrameCount
	408	"""
	409
360	410	return theTiffReport
361	411	validateTiff = classmethod(validateTiff)
362	412
	413	def validateTiffImageData(self, inImage, ):
	414	"""
	415	Examines the tiff image data to compare with
	416	"""
	417
	418	""" code to look at the list of tiff image dimensions
	419	theTiffWidth = None
	420	theTiffHeight = None
	421	try:
	422	#theTiffWidth = int(inImage.tag[256])
	423	print inImage.tag[256]
	424	except KeyError:
	425	pass
	426	except ValueError:
	427	pass
	428	try:
	429	theTiffHeight = int(inImage.tag[257])
	430	except KeyError:
	431	pass
	432	except ValueError:
	433	pass
	434	"""
	435
	436	#look for frames
	437	self.tiffFileFrames = 0
	438	try:
	439	while True:
	440	inImage.seek( self.tiffFileFrames )
	441	self.tiffFileFrames = self.tiffFileFrames + 1
	442	except EOFError:
	443	inImage.seek( 0 )
	444	pass
	445
	446	self.isOmeTiffConsistent = True
	447
	448	# compare with values from xml and tiff
	449	if self.tiffFileFrames > self.ome5dPlaneCount:
	450	self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s needing %s" % (self.tiffFileFrames,self.ome5dPlaneCount)) , "Extra frames are present in this Tiff file"))
	451
	452	if self.tiffFileFrames < self.ome5dPlaneCount:
	453	self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s out of %s" % (self.tiffFileFrames,self.ome5dPlaneCount)) , "Not all possible frames are present in this Tiff file"))
	454
	455	# compare with values from xml TiffData and tiff
	456	totalTiffDataFrames = self.omeTiffDataPlaneCount + (self.tiffFileFrames * self.theAllFrameCount)
	457	if self.tiffFileFrames > totalTiffDataFrames:
	458	self.warningList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s referenced %s" % (self.tiffFileFrames,totalTiffDataFrames)) , "Unreferenced frames are present in this Tiff file"))
	459
	460	if self.tiffFileFrames < totalTiffDataFrames:
	461	self.errorList.append(ParseMessage(None, None, None, "TIFF", ("Frames %s out of %s" % (self.tiffFileFrames,totalTiffDataFrames)) , "Not all required frames are present in this Tiff file"))
	462	self.isOmeTiffConsistent = False
363	463
364	464	# Used by sax parser to handle errors when processing Elements
…	…
399	499	self.inBinDataContent = False
400	500	self.shortFormXml = ""
	501	# internal check counters
401	502	self.skipCount = 0
	503	self.omeTiffDataCount = 0
	504	self.omePixelsCount = 0
	505	self.omePlanesCount = 0
	506	self.ome5dPlaneCount = 0
	507	self.omeTiffDataPlaneCount = 0
	508	self.theAllFrameCount = 0
402	509	self.hasCustomAttributes = False
403	510
…	…
486	593	if name[-7:] == "BinData":
487	594	self.inBinData = True
	595
	596	if name[-8:] == "TiffData":
	597	self.omeTiffDataCount = self.omeTiffDataCount + 1
	598	# record the number of planes used by the TiffData block
	599	if "NumPlanes" in attribs:
	600	# use the number of planes specified
	601	self.omeTiffDataPlaneCount = self.omeTiffDataPlaneCount + int(attribs.getValue("NumPlanes"))
	602	if self.theAllFrameCount > 0:
	603	self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 1]"))
	604
	605	else:
	606	if "IFD" in attribs:
	607	# use one frame
	608	self.omeTiffDataPlaneCount = self.omeTiffDataPlaneCount + 1
	609	if self.theAllFrameCount > 0:
	610	self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 2]"))
	611	else:
	612	# use all the frames in the tiff
	613	self.theAllFrameCount = self.theAllFrameCount + 1
	614	if (self.theAllFrameCount > 1) or (self.omeTiffDataPlaneCount > 0):
	615	self.errorList.append(ParseMessage(None, None, None, "OME","", "Inconsistent use of TiffData element [Type 3]"))
	616
	617	if name[-6:] == "Pixels":
	618	self.omePixelsCount = self.omePixelsCount + 1
	619	try:
	620	# total up planes needed from Z, C and T
	621	theZ = int(attribs.getValue("SizeZ"))
	622	theC = int(attribs.getValue("SizeC"))
	623	theT = int(attribs.getValue("SizeT"))
	624	# print "Z: %s, C: %s, T: %s" % (theZ, theC, theT)
	625	self.ome5dPlaneCount = self.ome5dPlaneCount + (theZ * theC * theT)
	626	except KeyError:
	627	pass
	628	except ValueError:
	629	pass
	630
	631	if name[-5:] == "Plane":
	632	self.omePlanesCount = self.omePlanesCount + 1
	633
488	634	self.domify(name, attribs)
489	635
…	…
556	702
557	703	if __name__ == '__main__':
558		for aFilename in ["samples/sdub.ome", "samples/tiny.ome", "samples/broke.ome"]:
559		print "============ XML file %s ============ " % aFilename
560		print XmlReport.validateFile(aFilename)
	704	for aFilename in ["samples/completesamplenopre.xml","samples/completesample.xml","samples/completesamplenoenc.xml",
	705	"samples/sdub.ome", "samples/sdub-fix.ome", "samples/sdub-fix-pre.ome",
	706	"samples/tiny.ome", "samples/broke.ome"]:
	707	print "============ XML file %s ============ " % aFilename
	708	print XmlReport.validateFile(aFilename)
	709
561	710
562	711	for aFilename in ["samples/4d2wOME.tif", "samples/4d2wOME-fixed.tif",
…	…
567	716
568	717	print "============"
569
570

Xml/Working

Property svn:ignore

old	new
1	1	.DS_Store
2	2	Working Project.tmproj
	3	ClareQuestions.xml

Xml/Working/AnalysisModule.xsd

r71	r93
415	415	<simpleType name = "ModuleID">
416	416	<restriction base = "OME:LSID">
417		<pattern value = "(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:Module:\S+)\|(Module:\S+)"/>
	417	<pattern value = "(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Module:\S+)\|(Module:\S+)"/>
418	418	</restriction>
419	419	</simpleType>

Xml/Working/SPW.xsd

r68	r93
98	98	<xsd:simpleType name="PlateID">
99	99	<xsd:restriction base="OME:LSID">
100		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:Plate:\S+)\|(Plate:\S+)"/>
	100	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Plate:\S+)\|(Plate:\S+)"/>
101	101	</xsd:restriction>
102	102	</xsd:simpleType>
…	…
147	147	<xsd:simpleType name="ReagentID">
148	148	<xsd:restriction base="OME:LSID">
149		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:Reagent:\S+)\|(Reagent:\S+)"/>
	149	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Reagent:\S+)\|(Reagent:\S+)"/>
150	150	</xsd:restriction>
151	151	</xsd:simpleType>
…	…
215	215	<xsd:simpleType name="ScreenID">
216	216	<xsd:restriction base="OME:LSID">
217		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:Screen:\S+)\|(Screen:\S+)"/>
	217	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Screen:\S+)\|(Screen:\S+)"/>
218	218	</xsd:restriction>
219	219	</xsd:simpleType>
…	…
269	269	<xsd:simpleType name="ScreenAcquisitionID">
270	270	<xsd:restriction base="OME:LSID">
271		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:ScreenAcquisition:\S+)\|(ScreenAcquisition:\S+)"/>
	271	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:ScreenAcquisition:\S+)\|(ScreenAcquisition:\S+)"/>
272	272	</xsd:restriction>
273	273	</xsd:simpleType>
…	…
333	333	<xsd:simpleType name="WellID">
334	334	<xsd:restriction base="OME:LSID">
335		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:Well:\S+)\|(Well:\S+)"/>
	335	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:Well:\S+)\|(Well:\S+)"/>
336	336	</xsd:restriction>
337	337	</xsd:simpleType>
…	…
381	381	<xsd:simpleType name="WellSampleID">
382	382	<xsd:restriction base="OME:LSID">
383		<xsd:pattern value="(urn:lsid:([\w~~-\.]+\.[\w~~-\.]+)+:WellSample:\S+)\|(WellSample:\S+)"/>
	383	<xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:WellSample:\S+)\|(WellSample:\S+)"/>
384	384	</xsd:restriction>
385	385	</xsd:simpleType>

Xml/Working/ome.xsd

r73	r93
24	24	xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2007-06"
25	25	xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2007-06"
26		version="1"
	26	version="2"
27	27	elementFormDefault="qualified">
28	28	<xsd:import namespace="http://www.openmicroscopy.org/Schemas/AnalysisModule/2007-06" schemaLocation="http://www.openmicroscopy.org/Schemas/AnalysisModule/2007-06/AnalysisModule.xsd"/>
…	…
34	34	<xsd:documentation>
35	35	Open Microscopy Environment
36		OME XML Schema ~~2.0-RC1~~
	36	OME XML Schema June 2007 - Update Version 2 September 2007
37	37	Author: Ilya G. Goldberg, Andrew J Patterson
38	38	Copyright 2002 - 2007 OME. All rights reserved.
…	…
685	685	<xsd:sequence>
686	686	<xsd:element ref="Microscope"/>
687		<xsd:element ref="LightSource" maxOccurs="unbounded"/>
688		<xsd:element ref="Detector" maxOccurs="unbounded"/>
689		<xsd:element ref="Objective" maxOccurs="unbounded"/>
	687	<xsd:element ref="LightSource" minOccurs="0" maxOccurs="unbounded"/>
	688	<xsd:element ref="Detector" minOccurs="0" maxOccurs="unbounded"/>
	689	<xsd:element ref="Objective" minOccurs="0" maxOccurs="unbounded"/>
690	690	<xsd:element ref="FilterSet" minOccurs="0" maxOccurs="unbounded"/>
691	691	<xsd:element ref="Filter" minOccurs="0" maxOccurs="unbounded"/>
692	692	<xsd:element ref="Dichroic" minOccurs="0" maxOccurs="unbounded"/>
693		<xsd:element ref="OTF" maxOccurs="unbounded"/>
	693	<xsd:element ref="OTF" minOccurs="0" maxOccurs="unbounded"/>
694	694	</xsd:sequence>
695	695	<xsd:attribute name="ID" use="required" type="InstrumentID"/>
…	…
709	709	</xsd:complexType>
710	710	</xsd:element>
711		<xsd:element name="Experimenter" ~~type="ExperimenterType"~~>
	711	<xsd:element name="Experimenter">
712	712	<xsd:annotation>
713	713	<xsd:documentation>
…	…
715	715	This person may also be a user of the OME system, in which case the OMEName element contains their login name.
716	716	Experimenters may belong to one or more groups which are specified using one or more GroupRef elements.
717		</xsd:documentation>
718		</xsd:annotation>
	717	Note while FirstName, LastName, Email and OMEName are all optional to be valid an Experimenter must have AT LEAST ONE present
	718	</xsd:documentation>
	719	</xsd:annotation>
	720	<xsd:complexType>
	721	<xsd:sequence>
	722	<xsd:choice>
	723	&nbs