def getDataset(self, index):
'''Retrieve a dataset from the DM file.
Note: Most DM3 and DM4 files contain a small "thumbnail" as the first dataset written as RGB data. This function ignores that dataset if it exists. To retrieve the thumbnail use the getThumbnail() function
'''
#The first dataset is usually a thumbnail. Test for this and skip the thumbnail automatically
if self.numObjects == 1:
ii = index
else:
ii = index + 1
#Check that the dataset exists.
try:
self._checkIndex(ii)
except:
raise
self.seek(self.fid, self.dataOffset[ii],0) #Seek to start of dataset from beginning of the file
outputDict = {}
outputDict['filename'] = osBasename(self.filename)
#Parse the dataset to see what type it is (image, image series, spectra, etc.)
if self.xSize[ii] > 0:
pixelCount = self.xSize[ii]*self.ySize[ii]*self.zSize[ii]*self.zSize2[ii]
jj = 0 #counter to determine where the first scale value starts
for nn in self.dataShape[0:ii]:
jj += nn #sum up all number of dimensions for previous datasets
#if self.dataType == 23: #RGB image(s)
# temp = self.fromfile(self.fid,count=pixelCount,dtype=np.uint8).reshape(self.ysize[ii],self.xsize[ii])
if self.zSize[ii] == 1: #2D data
outputDict['data'] = self.fromfile(self.fid,count=pixelCount,dtype=self._DM2NPDataType(self.dataType[ii])).reshape((self.ySize[ii],self.xSize[ii]))
outputDict['pixelUnit'] = self.scaleUnit[jj:jj+self.dataShape[ii]][::-1] #need to reverse the order to match the C-ordering of the data
outputDict['pixelSize'] = self.scale[jj:jj+self.dataShape[ii]][::-1]
outputDict['pixelOrigin'] = self.origin[jj:jj+self.dataShape[ii]][::-1]
elif self.zSize2[ii] > 1: #4D data
outputDict['data'] = self.fromfile(self.fid,count=pixelCount,dtype=self._DM2NPDataType(self.dataType[ii])).reshape((self.zSize2[ii],self.zSize[ii],self.ySize[ii],self.xSize[ii]))
outputDict['pixelUnit'] = self.scaleUnit[jj:jj+self.dataShape[ii]][::-1] #need to reverse the order to match the C-ordering of the data
outputDict['pixelSize'] = self.scale[jj:jj+self.dataShape[ii]][::-1]
outputDict['pixelOrigin'] = self.origin[jj:jj+self.dataShape[ii]][::-1]
else: #3D array
outputDict['data'] = self.fromfile(self.fid,count=pixelCount,dtype=self._DM2NPDataType(self.dataType[ii])).reshape((self.zSize[ii],self.ySize[ii],self.xSize[ii]))
outputDict['pixelUnit'] = self.scaleUnit[jj:jj+self.dataShape[ii]][::-1] #need to reverse the order to match the C-ordering of the data
outputDict['pixelSize'] = self.scale[jj:jj+self.dataShape[ii]][::-1]
outputDict['pixelOrigin'] = self.origin[jj:jj+self.dataShape[ii]][::-1]
return outputDict
def getSlice(self, index, sliceZ, sliceZ2=0):
'''Retrieve a slice of a dataset from the DM file. The data set will have a shape according to
3D = [sliceZ,Y,X] or 4D: [sliceZ2,sliceZ,Y,X]
Note: Most DM3 and DM4 files contain a small "thumbnail" as the first dataset written as RGB data. This function ignores that dataset if it exists. To retrieve the thumbnail use the getThumbnail() function.
Warning: DM4 files with 4D data sets are written as [X,Y,Z1,Z2]. This code currently gets the [X,Y] slice.
Getting the [Z1,Z2] slice is not yet implemented.
Parameters:
index (int): The number of the dataset in the DM file.
sliceZ (int): The slice to get along the first dimension (C-ordering) for 3D datasets or the 2nd dimensions for
Keywords:
sliceZ2 (int): For 4D dataset
Returns:
(dict): a dictionary containing meta data and the data.
'''
#The first dataset is usually a thumbnail. Test for this and skip the thumbnail automatically
if self.numObjects == 1:
ii = index
else:
ii = index + 1
#Check that the dataset exists.
try:
self._checkIndex(ii)
except:
raise
# Check sliceZ and sliceZ2 are within the data arrray size bounds
if sliceZ > (self.zSize[ii] - 1):
raise IndexError(
'Index out of range, trying to access element {} of {} valid elements'
.format(sliceZ, self.zSize))
if sliceZ2 > (self.zSize2[ii] - 1):
raise IndexError(
'Index out of range, trying to access element {} of {} valid elements'
.format(sliceZ2, self.zSize2))
self.seek(self.fid, self.dataOffset[ii],
0) #Seek to start of dataset from beginning of the file
outputDict = {}
outputDict['filename'] = osBasename(self.filename)
#Parse the dataset to see what type it is (image, 3D image series, spectra, 4D, etc.)
if self.xSize[ii] > 0:
#determine the number of bytes to skip
pixelCount = int(self.xSize[ii]) * int(self.ySize[ii])
byteCount = pixelCount * np.dtype(
self._DM2NPDataType(self.dataType[ii])).itemsize
jj = 0 #counter to determine where the first scale value starts
for nn in self.dataShape[0:ii]:
jj += nn #sum up all number of dimensions for previous datasets
if self.zSize[ii] == 1: #2D data
outputDict['data'] = self.fromfile(
self.fid,
count=pixelCount,
dtype=self._DM2NPDataType(self.dataType[ii])).reshape(
(self.ySize[ii], self.xSize[ii]))
elif self.zSize2[ii] > 1: #4D data
self.seek(self.fid, sliceZ * sliceZ2 * byteCount,
1) #skip ahead from current position
outputDict['data'] = self.fromfile(
self.fid,
count=pixelCount,
dtype=self._DM2NPDataType(self.dataType[ii])).reshape(
(self.ySize[ii], self.xSize[ii]))
else: #3D array
self.seek(self.fid, sliceZ * byteCount,
1) #skip ahead from current position
outputDict['data'] = self.fromfile(
self.fid,
count=pixelCount,
dtype=self._DM2NPDataType(self.dataType[ii])).reshape(
(self.ySize[ii], self.xSize[ii]))
#Return the proper meta data for this one image
outputDict['pixelUnit'] = self.scaleUnit[
jj:jj +
2][::
-1] #need to reverse the order to match the C-ordering of the data
outputDict['pixelSize'] = self.scale[jj:jj + 2][::-1]
outputDict['pixelOrigin'] = self.origin[jj:jj + 2][::-1]
return outputDict
