new tag

CMakeLists.txt

@@ -272,7 +272,7 @@ if (VISUS_PYTHON)
 	AddOpenVisusTest(VisusTestPyDataflow   COMMAND "${PYTHON_EXECUTABLE}"    "Samples/python/Dataflow.py"        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 	AddOpenVisusTest(VisusTestPyArray      COMMAND "${PYTHON_EXECUTABLE}"    "Samples/python/Array.py"           WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 	AddOpenVisusTest(VisusTestPyIdx        COMMAND "${PYTHON_EXECUTABLE}"    "Samples/python/Idx.py"             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-	AddOpenVisusTest(VisusTestPyXIdx       COMMAND "${PYTHON_EXECUTABLE}"    "Samples/python/Idx.py"             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+	AddOpenVisusTest(VisusTestPyXIdx       COMMAND "${PYTHON_EXECUTABLE}"    "Samples/python/XIdx.py"            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 
 	AddOpenVisusTest(VisusDataConversion1 COMMAND "${PYTHON_EXECUTABLE}"     "Samples/python/DataConversion1.py" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 	AddOpenVisusTest(VisusDataConversion2 COMMAND "${PYTHON_EXECUTABLE}"     "Samples/python/DataConversion2.py" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

Samples/python/Array.py

@@ -105,9 +105,7 @@ def test4(self):
 	print("All done")
 	SetCommandLine("__main__")
 	KernelModule.attach()
-	errors=unittest.main(exit=False).result.errors
+	unittest.main(exit=True)
 	KernelModule.detach()
-	print("All done ("+str(len(errors))+" errors)")
-	sys.exit(len(errors)>0)
 
 

Samples/python/DataConversion1.py

@@ -89,4 +89,5 @@
 		# ArrayUtils.saveImageUINT8("tmp/slice%d.offset.png" % (Z,),Array.fromNumPy(fill))
 
 	IdxModule.detach()
-	print("Done with conversion")
+	print("Done with conversion")
+	sys.exit(0)

Samples/python/DataConversion2.py

@@ -1 +1,122 @@
-import sysimport numpy as npfrom OpenVisus import *if __name__ == '__main__':		"""	Example of data conversion		Input is composed of 3 images, one for each channel (RGB)	each channel it's a 3d array		Ouput is an IDX		For each source slice the original data is shifted by 5 pixels:		first  slice is shifted by ( 0,0)		second slice is shifted by ( 5,0)		third  slice is shifted by (10,0)			"""	SetCommandLine("__main__")	IdxModule.attach()	# trick to speed up the conversion	os.environ["VISUS_DISABLE_WRITE_LOCK"]="1"		# 3 channels (RGB) each one is a 3d array	width,height,depth=2,3,4	channels = [	    np.zeros((depth,height,width),dtype=np.uint8)	,	    np.zeros((depth,height,width),dtype=np.uint8)	,	    np.zeros((depth,height,width),dtype=np.uint8)	,	]	              	idx_filename='visus.idx'	# for each slize along Z axis I shift the original data of offset[0],offset[1],offset[2] (like a shear)	offset = (5,0,0)	dataset,access,fields=None,None,None	for ChannelId,channel in enumerate(channels):	    # scrgiorgio: just for testing, if I get a 2d image instead of a 3d image stack I simulate a stack	    if len(channel.shape)==2: 	        channel=np.stack([channel]*7)	    	    dims=list(reversed(channel.shape))	    	    # numpy dtype -> OpenVisus dtype	    typestr=channel.__array_interface__["typestr"]	    dtype=DType(typestr[1]=="u", typestr[1]=="f", int(typestr[2])*8)        	    	    idx_logic_box=BoxNi(PointNi(0,0,0),PointNi(	            dims[0]+ offset[0]*dims[2],	            dims[1]+ offset[1]*dims[2],	            dims[2]+ offset[2]*dims[2]))	            	    # create the idx 	    if ChannelId==0:	        print("Creating idx file")	        idx_file = IdxFile()	        idx_file.logic_box=idx_logic_box	        print("\tbox",idx_logic_box.toString())	        	        # assuming all the files are the same type	        for I in range(len(channels)): 	            field=Field('channel_%d' % (I,),dtype)	            print("\tfield",field.name,field.dtype.toString())	            idx_file.fields.push_back(field)	        	        if not idx_file.save(idx_filename):	        	raise Exception("Cannot save idx")   	        		        dataset = LoadDataset(idx_filename)	        if not dataset: raise Exception("Cannot load idx")	        		        access = dataset.createAccess()	        if not access: raise Exception("Cannot create access")	        		        fields=idx_file.fields	        	    else:	        # check dimensions and dtype are compatible	        if not (dataset.getLogicBox()==idx_logic_box):	        	raise Exception("Logic box is wrong")	        		        if not (dtype==fields[ChannelId].dtype):	        	raise Exception("dtype is wrong")	        	    print("Adding","channel",ChannelId,"dims",dims,"dtype",dtype.toString())  	        	    # Now we go through each slice and add them one by one since we have to take care of the offset	    for Z in range(0,dims[2]):	    	        # target area in idx (i.e. apply a shear)	        x1,x2 = 0+offset[0]*Z , dims[0]+offset[0]*Z	        y1,y2 = 0+offset[1]*Z , dims[1]+offset[1]*Z	        z1,z2 = Z+offset[2]*Z , Z+1    +offset[2]*Z	      	        print("\tProcessing Z",Z,"target_p1",(x1, y1, z1),"target_p2",(x2, y2, z2))	               	        query = BoxQuery(dataset,dataset.getDefaultField(),dataset.getDefaultTime(),ord('w')) 	        query.logic_box = BoxNi(PointNi(x1,y1,z1),PointNi(x2,y2,z2))	        query.field = fields[ChannelId] 	        dataset.beginQuery(query)	        	        if not query.isRunning():	        	raise Exception("Begin query failed")	        		        query.buffer=Array.fromNumPy(channel[Z,:,:],bShareMem=True)	        		        if not dataset.executeQuery(access,query):	        	raise Exception("Cannot execute query")	        		IdxModule.detach()	print("Done with conversion")
+import sys
+import numpy as np
+from OpenVisus import *
+
+
+if __name__ == '__main__':
+
+	"""
+	Example of data conversion
+	
+	Input is composed of 3 images, one for each channel (RGB)
+	each channel it's a 3d array
+	
+	Ouput is an IDX
+	
+	For each source slice the original data is shifted by 5 pixels:
+		first  slice is shifted by ( 0,0)
+		second slice is shifted by ( 5,0)
+		third  slice is shifted by (10,0)	
+	
+	"""
+
+	SetCommandLine("__main__")
+	IdxModule.attach()
+
+	# trick to speed up the conversion
+	os.environ["VISUS_DISABLE_WRITE_LOCK"]="1"
+
+	# 3 channels (RGB) each one is a 3d array
+	width,height,depth=2,3,4
+
+	channels = [
+	    np.zeros((depth,height,width),dtype=np.uint8)	,
+	    np.zeros((depth,height,width),dtype=np.uint8)	,
+	    np.zeros((depth,height,width),dtype=np.uint8)	,
+	]
+
+	idx_filename='visus.idx'
+
+	# for each slize along Z axis I shift the original data of offset[0],offset[1],offset[2] (like a shear)
+	offset = (5,0,0)
+
+	dataset,access,fields=None,None,None
+
+	for ChannelId,channel in enumerate(channels):
+
+	    # scrgiorgio: just for testing, if I get a 2d image instead of a 3d image stack I simulate a stack
+	    if len(channel.shape)==2: 
+	        channel=np.stack([channel]*7)
+
+	    dims=list(reversed(channel.shape))
+
+	    # numpy dtype -> OpenVisus dtype
+	    typestr=channel.__array_interface__["typestr"]
+	    dtype=DType(typestr[1]=="u", typestr[1]=="f", int(typestr[2])*8)        
+
+	    idx_logic_box=BoxNi(PointNi(0,0,0),PointNi(
+	            dims[0]+ offset[0]*dims[2],
+	            dims[1]+ offset[1]*dims[2],
+	            dims[2]+ offset[2]*dims[2]))
+
+	    # create the idx 
+	    if ChannelId==0:
+	        print("Creating idx file")
+	        idx_file = IdxFile()
+	        idx_file.logic_box=idx_logic_box
+	        print("\tbox",idx_logic_box.toString())
+
+	        # assuming all the files are the same type
+	        for I in range(len(channels)): 
+	            field=Field('channel_%d' % (I,),dtype)
+	            print("\tfield",field.name,field.dtype.toString())
+	            idx_file.fields.push_back(field)
+
+	        if not idx_file.save(idx_filename):
+	        	raise Exception("Cannot save idx")   
+
+	        dataset = LoadDataset(idx_filename)
+	        if not dataset: raise Exception("Cannot load idx")
+
+	        access = dataset.createAccess()
+	        if not access: raise Exception("Cannot create access")
+
+	        fields=idx_file.fields
+
+	    else:
+	        # check dimensions and dtype are compatible
+	        if not (dataset.getLogicBox()==idx_logic_box):
+	        	raise Exception("Logic box is wrong")
+
+	        if not (dtype==fields[ChannelId].dtype):
+	        	raise Exception("dtype is wrong")
+
+	    print("Adding","channel",ChannelId,"dims",dims,"dtype",dtype.toString())  
+
+	    # Now we go through each slice and add them one by one since we have to take care of the offset
+	    for Z in range(0,dims[2]):
+
+	        # target area in idx (i.e. apply a shear)
+	        x1,x2 = 0+offset[0]*Z , dims[0]+offset[0]*Z
+	        y1,y2 = 0+offset[1]*Z , dims[1]+offset[1]*Z
+	        z1,z2 = Z+offset[2]*Z , Z+1    +offset[2]*Z
+
+	        print("\tProcessing Z",Z,"target_p1",(x1, y1, z1),"target_p2",(x2, y2, z2))
+
+	        query = BoxQuery(dataset,dataset.getDefaultField(),dataset.getDefaultTime(),ord('w')) 
+	        query.logic_box = BoxNi(PointNi(x1,y1,z1),PointNi(x2,y2,z2))
+	        query.field = fields[ChannelId] 
+	        dataset.beginQuery(query)
+
+	        if not query.isRunning():
+	        	raise Exception("Begin query failed")
+
+	        query.buffer=Array.fromNumPy(channel[Z,:,:],bShareMem=True)
+
+	        if not dataset.executeQuery(access,query):
+	        	raise Exception("Cannot execute query")
+
+
+	IdxModule.detach()
+	print("Done with conversion")
+	sys.exit(0)

Samples/python/Dataflow.py

@@ -124,8 +124,6 @@ def testDataflow(self):
 	DataflowModule.attach()
 	VISUS_REGISTER_NODE_CLASS("PyProducer")
 	VISUS_REGISTER_NODE_CLASS("PyReceiver")
-	errors=unittest.main(exit=False).result.errors
+	unittest.main(exit=True)
 	DataflowModule.detach()
-	print("All done ("+str(len(errors))+" errors)")
-	sys.exit(len(errors)>0)
 

Samples/python/Idx.py

@@ -63,7 +63,7 @@ def WriteIdx(self):
 		dataset_box=BoxNi(PointNi(0,0,0),PointNi(16,16,16))
 
 		idxfile=IdxFile();
-		idxfile.box=BoxNi(dataset_box)
+		idxfile.logic_box=BoxNi(dataset_box)
 		idxfile.fields.push_back(Field("myfield",DType.fromString("uint32")))
 
 		bSaved=idxfile.save(self.filename)
@@ -78,12 +78,12 @@ def WriteIdx(self):
 			slice_box=dataset.getLogicBox().getZSlab(Z,Z+1)
 
 			query=BoxQuery(dataset,dataset.getDefaultField(),dataset.getDefaultTime(),ord('w'))
-			query.logic_position=Position(slice_box)
+			query.logic_box=slice_box
 			dataset.beginQuery(query)
 			self.assertTrue(query.isRunning())
-			self.assertEqual(query.nsamples.innerProduct(),16*16)
+			self.assertEqual(query.getNumberOfSamples().innerProduct(),16*16)
 
-			buffer=Array(query.nsamples,query.field.dtype)
+			buffer=Array(query.getNumberOfSamples(),query.field.dtype)
 			query.buffer=buffer
 
 			fill=Array.toNumPy(buffer,bSqueeze=True,bShareMem=True)
@@ -108,10 +108,10 @@ def ReadIdx(self):
 			slice_box=box.getZSlab(Z,Z+1)
 
 			query=BoxQuery(dataset,dataset.getDefaultField(),dataset.getDefaultTime(),ord('r'))
-			query.logic_position=Position(slice_box)
+			query.logic_box=slice_box
 			dataset.beginQuery(query)
 			self.assertTrue(query.isRunning())
-			self.assertEqual(query.nsamples.innerProduct(),16*16)
+			self.assertEqual(query.getNumberOfSamples().innerProduct(),16*16)
 			self.assertTrue(dataset.executeQuery(access,query))
 
 			check=Array.toNumPy(query.buffer,bSqueeze=True,bShareMem=True)
@@ -136,20 +136,21 @@ def MergeIdx(self):
 
 		#create and read data from VisusFIle up to resolution FinalH=8 (<MaxH)
 		query=BoxQuery(dataset,dataset.getDefaultField(),dataset.getDefaultTime(),ord('r'))
-		query.logic_position=Position(slice_box)
-		query.end_resolutions={8,12}
+		query.logic_box=slice_box
+		query.end_resolutions.push_back(8)
+		query.end_resolutions.push_back(12)
 
 		# end_resolution=8
 		dataset.beginQuery(query)
 		self.assertTrue(query.isRunning())
-		self.assertTrue(query.nsamples.innerProduct()>0)
+		self.assertTrue(query.getNumberOfSamples().innerProduct()>0)
 		self.assertTrue(dataset.executeQuery(access,query))
 		self.assertEqual(query.getCurrentResolution(),8)
 
 		# end_resolution=12
 		dataset.nextQuery(query)
 		self.assertTrue(query.isRunning())
-		self.assertEqual(query.nsamples.innerProduct(),16*16)
+		self.assertEqual(query.getNumberOfSamples().innerProduct(),16*16)
 		self.assertTrue(dataset.executeQuery(access,query))
 		self.assertEqual(query.getCurrentResolution(),12)
 
@@ -166,8 +167,5 @@ def MergeIdx(self):
 if __name__ == '__main__':
 	SetCommandLine("__main__")
 	IdxModule.attach()
-	errors=unittest.main(exit=False).result.errors
+	unittest.main(exit=True)
 	IdxModule.detach()
-	print("All done ("+str(len(errors))+" errors)")
-	sys.exit(len(errors)>0)
-

Samples/python/Server.py

@@ -71,5 +71,6 @@ def runSingleDatasetServer(name,idx_filename,port=10000,dynamic=False):
 	else:
 		IdxModule.detach()
 
+	sys.exit(0)
 
 

Samples/python/XIdx.py

@@ -171,6 +171,6 @@ def VerifyXIdx(self):
 if __name__ == '__main__':
 	SetCommandLine("__main__")
 	XIdxModule.attach()
-	unittest.main(exit=False)
+	unittest.main(exit=True)
 	XIdxModule.detach()
 	print("All done")

conda/openvisus/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openvisus
-  version: 1.3.65
+  version: 1.3.66
 
 source:
   path: ../..

datasets/google_and_slam.midx

@@ -9,7 +9,7 @@
 
 
 	<!-- already in 0,1 range  -->
-	<dataset name='slam' url='D:/google_sci/visus_slam/Alfalfa/VisusSlamFiles/visus.midx' />
+	<dataset name='slam' url='D:/GoogleSci/visus_slam/Alfalfa/VisusSlamFiles/visus.midx' />
 
 </dataset>