def _mergeTif(self, parts, outfilename):
for i, tifname in enumerate(parts):
tif = TiffIO.TiffIO(tifname, mode='rb')
nImages = tif.getNumberOfImages()
if i == 0:
images = [tif.getData(j).copy() for j in range(nImages)]
headers = [{
'Title': tif.getInfo(j)['info']['Title']
} for j in range(nImages)]
else:
headersi = [{
'Title': tif.getInfo(j)['info']['Title']
} for j in range(nImages)]
for header, img in zip(headers, images):
k = headersi.index(header)
self._fillPartial(img, tif.getData(k))
del tif
if os.path.exists(outfilename):
_logger.debug("Output file already exists, trying to delete it")
os.remove(outfilename)
for i, (img, header) in enumerate(zip(images, headers)):
# TODO: there must be a better way
if i == 0:
tifout = TiffIO.TiffIO(outfilename, mode="wb+")
elif i == 1:
del tifout
tifout = TiffIO.TiffIO(outfilename, mode="rb+")
tifout.writeImage(img, info=header)
del tifout
def save3DArrayAsMonochromaticTiff(data,
filename,
labels=None,
dtype=None,
mcaindex=-1):
ndata = data.shape[mcaindex]
if dtype is None:
dtype = numpy.float32
if os.path.exists(filename):
try:
os.remove(filename)
except OSError:
pass
if labels is None:
labels = []
for i in range(ndata):
labels.append("Array_%d" % i)
if len(labels) != ndata:
raise ValueError("Incorrect number of labels")
outfileInstance = TiffIO.TiffIO(filename, mode="wb+")
if mcaindex in [2, -1]:
for i in range(ndata):
if i == 1:
outfileInstance = TiffIO.TiffIO(filename, mode="rb+")
if dtype is None:
tmpData = data[:, :, i]
else:
tmpData = data[:, :, i].astype(dtype)
outfileInstance.writeImage(tmpData, info={'Title': labels[i]})
if (ndata > 10):
print("Saved image %d of %d" % (i + 1, ndata))
_logger.info("Saved image %d of %d", i + 1, ndata)
elif mcaindex == 1:
for i in range(ndata):
if i == 1:
outfileInstance = TiffIO.TiffIO(filename, mode="rb+")
if dtype is None:
tmpData = data[:, i, :]
else:
tmpData = data[:, i, :].astype(dtype)
outfileInstance.writeImage(tmpData, info={'Title': labels[i]})
if (ndata > 10):
_logger.info("Saved image %d of %d", i + 1, ndata)
print("Saved image %d of %d" % (i + 1, ndata))
else:
for i in range(ndata):
if i == 1:
outfileInstance = TiffIO.TiffIO(filename, mode="rb+")
if dtype is None:
tmpData = data[i]
else:
tmpData = data[i].astype(dtype)
outfileInstance.writeImage(tmpData, info={'Title': labels[i]})
if (ndata > 10):
_logger.info("Saved image %d of %d", i + 1, ndata)
print("Saved image %d of %d" % (i + 1, ndata))
outfileInstance.close() # force file close
def test():
from PyMca5 import StackBase
testFileName = "TiffTest.tif"
nrows = 2000
ncols = 2000
#create a dummy stack with 100 images
nImages = 100
imagestack = True
a = numpy.ones((nrows, ncols), numpy.float32)
if not os.path.exists(testFileName):
print("Creating test filename %s" % testFileName)
tif = TiffIO.TiffIO(testFileName, mode='wb+')
for i in range(nImages):
data = (a * i).astype(numpy.float32)
if i == 1:
tif = TiffIO.TiffIO(testFileName, mode='rb+')
tif.writeImage(data,
info={'Title': 'Image %d of %d' % (i + 1, nImages)})
tif = None
stackData = TiffStack(imagestack=imagestack)
stackData.loadFileList([testFileName], dynamic=True)
if 0:
stack = StackBase.StackBase()
stack.setStack(stackData)
print("This should be 0 = %f" %
stack.calculateROIImages(0, 0)['ROI'].sum())
print("This should be %f = %f" %\
(a.sum(),stack.calculateROIImages(1, 2)['ROI'].sum()))
if imagestack:
print("%f should be = %f" %\
(stackData.data[0:10,:,:].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI 10 should be = %f" %\
stackData.data[10:11,[10],11].sum())
print("Test small ROI 40 should be = %f" %\
stackData.data[10:11,[10,12,14,16],11].sum())
else:
print("%f should be = %f" %\
(stackData.data[:,:, 0:10].sum(),
stack.calculateROIImages(0, 10)['ROI'].sum()))
print("Test small ROI %f" %\
stackData.data[10:11,[29],:].sum())
else:
from PyMca5.PyMca import PyMcaQt as qt
from PyMca5.PyMca import QStackWidget
app = qt.QApplication([])
w = QStackWidget.QStackWidget()
print("Setting stack")
w.setStack(stackData)
w.show()
app.exec_()
def save2DArrayListAsMonochromaticTiff(datalist,
filename,
labels=None,
dtype=None):
if type(datalist) != type([]):
datalist = [datalist]
ndata = len(datalist)
if dtype is None:
dtype = datalist[0].dtype
for i in range(len(datalist)):
dtypeI = datalist[i].dtype
if dtypeI in [numpy.float32, numpy.float64] or\
dtypeI.str[-2] == 'f':
dtype = numpy.float32
break
elif dtypeI != dtype:
dtype = numpy.float32
break
if labels is None:
labels = []
for i in range(ndata):
labels.append("Array_%d" % i)
if len(labels) != ndata:
raise ValueError("Incorrect number of labels")
multifile = False
if type(filename) in [type([]), type((1, ))]:
if len(filename) == 1:
fileList = filename
elif len(filename) != len(labels):
raise ValueError("Incorrect number of files")
else:
fileList = filename
multifile = True
else:
fileList = [filename]
savedData = 0
while savedData < ndata:
if multifile:
fname = fileList[savedData]
else:
fname = fileList[0]
if os.path.exists(fname):
try:
os.remove(fname)
except OSError:
_logger.warning("Cannot remove file %s", fname)
pass
if (savedData == 0) or multifile:
outfileInstance = TiffIO.TiffIO(fname, mode="wb+")
if multifile:
# multiple files
if dtype is None:
data = datalist[savedData]
else:
data = datalist[savedData].astype(dtype)
outfileInstance.writeImage(data, info={'Title': labels[savedData]})
savedData += 1
else:
# a single file
for i in range(ndata):
if i == 1:
outfileInstance = TiffIO.TiffIO(fname, mode="rb+")
if dtype is None:
data = datalist[i]
else:
data = datalist[i].astype(dtype)
outfileInstance.writeImage(data, info={'Title': labels[i]})
savedData += 1
outfileInstance.close() # force file close
def __getitem__(self, args0):
standardSlice = True
indices = []
outputShape = []
scalarArgs = []
args = []
if not hasattr(args0, "__len__"):
args0 = [args0]
for i in range(len(self.__shape)):
if i < len(args0):
args.append(args0[i])
else:
args.append(slice(None, None, None))
for i in range(len(args)):
if isinstance(args[i], slice):
start = args[i].start
stop = args[i].stop
step = args[i].step
if start is None:
start = 0
if stop is None:
stop = self.__shape[i]
if step is None:
step = 1
if step < 1:
raise ValueError("Step must be >= 1 (got %d)" % step)
if start is None:
start = 0
if start < 0:
start = self.__shape[i]-start
if stop < 0:
stop = self.__shape[i]-stop
if stop == start:
raise ValueError("Zero-length selections are not allowed")
indices.append(list(range(start, stop, step)))
elif type(args[i]) == type([]):
if len(args[i]):
indices.append([int(x) for x in args[i]])
else:
standardSlice = False
elif type(args[i]) in [type(1), type(long(1))]:
start = args[i]
if start < 0:
start = self.__shape[i] - start
stop = start + 1
step = 1
start = args[i]
args[i] = slice(start, stop, step)
indices.append(list(range(start, stop, step)))
scalarArgs.append(i)
else:
standardSlice = False
if not standardSlice:
print("args = ", args)
raise NotImplemented("__getitem__(self, args) only works on slices")
if len(indices) < 3:
print("input args = ", args0)
print("working args = ", args)
print("indices = ", indices)
raise NotImplemented("__getitem__(self, args) only works on slices")
outputShape = [len(indices[0]), len(indices[1]), len(indices[2])]
outputArray = numpy.zeros(outputShape, dtype=self.__dtype)
# nbFiles = len(self.__fileList)
nImagesPerFile = self.__nImagesPerFile
if self.__imageStack:
i = 0
rowMin = min(indices[1])
rowMax = max(indices[1])
for imageIndex in indices[0]:
fileNumber = int(imageIndex/nImagesPerFile)
if fileNumber != self.__oldFileNumber:
self.__tmpInstance = TiffIO.TiffIO(self.__fileList[fileNumber],
mode='rb+')
self.__oldFileNumber = fileNumber
imageNumber = imageIndex % nImagesPerFile
imageData = self.__tmpInstance.getData(imageNumber,
rowMin=rowMin,
rowMax=rowMax)
try:
outputArray[i,:,:] = imageData[args[1],args[2]]
except:
print("outputArray[i,:,:].shape =",outputArray[i,:,:].shape)
print("imageData[args[1],args[2]].shape = " , imageData[args[1],args[2]].shape)
print("input args = ", args0)
print("working args = ", args)
print("indices = ", indices)
print("scalarArgs = ", scalarArgs)
raise
i += 1
else:
i = 0
rowMin = min(indices[0])
rowMax = max(indices[0])
for imageIndex in indices[-1]:
fileNumber = int(imageIndex/nImagesPerFile)
if fileNumber != self.__oldFileNumber:
self.__tmpInstance = TiffIO.TiffIO(self.__fileList[fileNumber],
mode='rb+')
self.__oldFileNumber = fileNumber
imageNumber = imageIndex % nImagesPerFile
imageData = self.__tmpInstance.getData(imageNumber,
rowMin=rowMin,
rowMax=rowMax)
outputArray[:,:, i] = imageData[args[0],args[1]]
i += 1
if len(scalarArgs):
finalShape = []
for i in range(len(outputShape)):
if i in scalarArgs:
continue
finalShape.append(outputShape[i])
outputArray.shape = finalShape
return outputArray
def loadFileList(self, filelist, dynamic=False, fileindex=0):
if type(filelist) != type([]):
filelist = [filelist]
#retain the file list
self.sourceName = filelist
#the number of files
nbFiles=len(filelist)
#the intance to access the first file
fileInstance = TiffIO.TiffIO(filelist[0])
#the number of images per file
nImagesPerFile = fileInstance.getNumberOfImages()
#get the dimensions from the image itself
tmpImage = fileInstance.getImage(0)
if self.__dtype is None:
self.__dtype = tmpImage.dtype
nRows, nCols = tmpImage.shape
#stack shape
if self.__imageStack:
shape = (nbFiles * nImagesPerFile, nRows, nCols)
else:
shape = (nRows, nCols, nbFiles * nImagesPerFile)
#we can create the stack
if not dynamic:
try:
data = numpy.zeros(shape,
self.__dtype)
except (MemoryError, ValueError):
dynamic = True
if not dynamic:
imageIndex = 0
self.onBegin(nbFiles * nImagesPerFile)
for i in range(nbFiles):
tmpInstance =TiffIO.TiffIO(filelist[i])
for j in range(nImagesPerFile):
tmpImage = tmpInstance.getImage(j)
if self.__imageStack:
data[imageIndex,:,:] = tmpImage
else:
data[:,:,imageIndex] = tmpImage
imageIndex += 1
self.incrProgressBar = imageIndex
self.onProgress(imageIndex)
self.onEnd()
if dynamic:
data = TiffArray(filelist,
shape,
self.__dtype,
imagestack=self.__imageStack)
self.info = {}
self.data = data
shape = self.data.shape
for i in range(len(shape)):
key = 'Dim_%d' % (i+1,)
self.info[key] = shape[i]
if self.__imageStack:
self.info["McaIndex"] = 0
self.info["FileIndex"] = 1
else:
self.info["McaIndex"] = 2
self.info["FileIndex"] = 0
self.info["SourceType"] = SOURCE_TYPE
self.info["SourceName"] = self.sourceName
