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update cilBaseCroppedReader as it failed
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@paskino
paskino committed Apr 15, 2024
1 parent cc854ba commit 7418344
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Showing 2 changed files with 146 additions and 82 deletions.
3 changes: 2 additions & 1 deletion Wrappers/Python/ccpi/viewer/CILViewerBase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,8 @@ def __init__(self, dimx=600, dimy=600, renWin=None, iren=None, ren=None, debug=F
ori.SetViewport(0.0, 0.0, 0.4, 0.4)
ori.SetEnabled(1)
ori.InteractiveOff()
self.orientation_marker = ori
self.orientation_marker_widget = ori
self.orientation_marker = om

# holder for list of actors and widgets
self.actors = {}
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225 changes: 144 additions & 81 deletions Wrappers/Python/ccpi/viewer/utils/conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,9 @@

import shutil

import logging
logger = logging.getLogger(__name__)


# Converter class
class Converter(object):
Expand Down Expand Up @@ -1448,7 +1451,7 @@ def __init__(self):
VTKPythonAlgorithmBase.__init__(self, nInputPorts=0, nOutputPorts=1)
super(cilBaseCroppedReader, self).__init__()
self._TargetZExtent = (0, 0)

def SetTargetZExtent(self, value):
'''
Set the target extent to crop to on the z axis.
Expand Down Expand Up @@ -1478,113 +1481,173 @@ def RequestData(self, request, inInfo, outInfo):

# get basic info
big_endian = self.GetBigEndian()
isBigEndian = big_endian

readshape = self.GetStoredArrayShape()
file_header_length = self.GetFileHeaderLength()
is_fortran = self.GetIsFortran()

bytes_per_element = Converter.vtkType_to_bytes[self.GetOutputVTKType()]

if is_fortran:
shape = list(readshape)
else:
shape = list(readshape)[::-1]

tmpdir = tempfile.mkdtemp()
header_filename = os.path.join(tmpdir, "header.mhd")
reader = vtk.vtkMetaImageReader()
reader.SetFileName(header_filename)

slice_length = self._GetSliceLengthInFile()

offset = 0
slice_size = -1

dimensionality = len(shape)

if dimensionality == 3:
# read the centre slice
slice_size = shape[1]*shape[0]
offset = shape[2]*slice_size//2

rawfname = os.path.join(tempfile.gettempdir(),"test.raw")

offset = offset * bytes_per_element
slices_to_read = 1
if shape[2] > 1:
slices_to_read = 2
try:
if self.GetTargetZExtent()[1] >= shape[2] and self.GetTargetZExtent()[0] <= 0:
# in this case we don't need to crop, so we read the whole dataset
# print("Don't crop")

chunk_file_name = os.path.join(tmpdir, "chunk.raw")

# Creates a metaimageheader which will be used to read a file containing the
# data - chunk_file_name which we will fill below.

cilNumpyMETAImageWriter.WriteMETAImageHeader(chunk_file_name,
header_filename,
self.GetMetaImageTypeCode(),
big_endian,
0,
tuple(shape),
spacing=tuple(self.GetElementSpacing()),
origin=self.GetOrigin())

image_file = self.GetFileName()
# Writes the entire dataset to chunk_file_name
with open(image_file, "rb") as image_file_object:
end_slice = shape[2]
chunk_location = file_header_length
with open(chunk_file_name, "wb") as chunk_file_object:
image_file_object.seek(chunk_location)
chunk_length = slice_length * end_slice
chunk = image_file_object.read(chunk_length)
chunk_file_object.write(chunk)
with open(self.GetFileName(), 'br') as f:
f.seek(offset)
raw_data = f.read(slice_size*bytes_per_element* slices_to_read)
with open(rawfname, 'wb') as f2:
f2.write(raw_data)

reader.Modified()
reader.Update()
# print(reader.GetOutput().GetScalarComponentAsDouble(0, 0, 0, 0))
outData.ShallowCopy(reader.GetOutput())
reader = vtk.vtkImageReader2()
reader.SetFileName(rawfname)

vtktype = self.GetOutputVTKType()
reader.SetDataScalarType(vtktype)

return 1

# In the case we do need to crop: ---------------------------------------------

shape[2] = self.GetTargetZExtent()[1] - self.GetTargetZExtent()[0] + 1

chunk_file_name = os.path.join(tmpdir, "chunk.raw")

# Creates a metaimageheader which will be used to read a file just containing the cropped
# data - chunk_file_name which we will fill below.
cilNumpyMETAImageWriter.WriteMETAImageHeader(chunk_file_name,
header_filename,
self.GetMetaImageTypeCode(),
big_endian,
0,
tuple(shape),
spacing=tuple(self.GetElementSpacing()),
origin=self.GetOrigin())
image_file = self.GetFileName()
chunk_location = file_header_length + \
(self.GetTargetZExtent()[0]) * slice_length

# Reads the data as a single chunk.
# Copies the chunk from the original file to chunk_file_name:
with open(chunk_file_name, "wb") as chunk_file_object:
with open(image_file, "rb") as image_file_object:
image_file_object.seek(chunk_location)
chunk_length = (self.GetTargetZExtent()[1] - self.GetTargetZExtent()[0] + 1) * slice_length
chunk = image_file_object.read(chunk_length)
chunk_file_object.write(chunk)

reader.Modified()
if isBigEndian:
reader.SetDataByteOrderToBigEndian()
else:
reader.SetDataByteOrderToLittleEndian()

reader.SetFileDimensionality(len(shape))
vtkshape = shape[:]
if not is_fortran:
# need to reverse the shape (again)
vtkshape = shape[::-1]
# vtkshape = shape[:]
slice_idx = 0
if dimensionality == 3:
slice_idx = vtkshape[2]//2
extent = (0, vtkshape[0]-1, 0, vtkshape[1]-1, slice_idx, slice_idx+slices_to_read-1)
reader.SetDataExtent(extent)
# DataSpacing and DataOrigin should be added to the interface
reader.SetDataSpacing(1, 1, 1)
reader.SetDataOrigin(0, 0, 0)

logger.info("reading")
reader.Update()

########################################
# if is_fortran:
# shape = list(readshape)
# else:
# shape = list(readshape)[::-1]

# tmpdir = tempfile.mkdtemp()
# header_filename = os.path.join(tmpdir, "header.mhd")
# reader = vtk.vtkMetaImageReader()
# reader.SetFileName(header_filename)

# slice_length = self._GetSliceLengthInFile()

# try:
# if self.GetTargetZExtent()[1] >= shape[2] and self.GetTargetZExtent()[0] <= 0:
# # in this case we don't need to crop, so we read the whole dataset
# # print("Don't crop")

# chunk_file_name = os.path.join(tmpdir, "chunk.raw")

# # Creates a metaimageheader which will be used to read a file containing the
# # data - chunk_file_name which we will fill below.

# cilNumpyMETAImageWriter.WriteMETAImageHeader(chunk_file_name,
# header_filename,
# self.GetMetaImageTypeCode(),
# big_endian,
# 0,
# tuple(shape),
# spacing=tuple(self.GetElementSpacing()),
# origin=self.GetOrigin())

# image_file = self.GetFileName()
# # Writes the entire dataset to chunk_file_name
# with open(image_file, "rb") as image_file_object:
# end_slice = shape[2]
# chunk_location = file_header_length
# with open(chunk_file_name, "wb") as chunk_file_object:
# image_file_object.seek(chunk_location)
# chunk_length = slice_length * end_slice
# chunk = image_file_object.read(chunk_length)
# chunk_file_object.write(chunk)

# reader.Modified()
# reader.Update()
# # print(reader.GetOutput().GetScalarComponentAsDouble(0, 0, 0, 0))
# outData.ShallowCopy(reader.GetOutput())

# return 1

# # In the case we do need to crop: ---------------------------------------------

# shape[2] = self.GetTargetZExtent()[1] - self.GetTargetZExtent()[0] + 1

# chunk_file_name = os.path.join(tmpdir, "chunk.raw")

# # Creates a metaimageheader which will be used to read a file just containing the cropped
# # data - chunk_file_name which we will fill below.
# cilNumpyMETAImageWriter.WriteMETAImageHeader(chunk_file_name,
# header_filename,
# self.GetMetaImageTypeCode(),
# big_endian,
# 0,
# tuple(shape),
# spacing=tuple(self.GetElementSpacing()),
# origin=self.GetOrigin())
# image_file = self.GetFileName()
# chunk_location = file_header_length + \
# (self.GetTargetZExtent()[0]) * slice_length

# # Reads the data as a single chunk.
# # Copies the chunk from the original file to chunk_file_name:
# with open(chunk_file_name, "wb") as chunk_file_object:
# with open(image_file, "rb") as image_file_object:
# image_file_object.seek(chunk_location)
# chunk_length = (self.GetTargetZExtent()[1] - self.GetTargetZExtent()[0] + 1) * slice_length
# chunk = image_file_object.read(chunk_length)
# chunk_file_object.write(chunk)

# reader.Modified()
# reader.Update()

# Once we have read the data, update the extent to reflect where
# we have cut the cropped dataset out of the original image
Data = vtk.vtkImageData()
extent = (0, shape[0] - 1, 0, shape[1] - 1, self.GetTargetZExtent()[0], self.GetTargetZExtent()[1])
Data.SetExtent(extent)
Data.SetSpacing(self.GetElementSpacing())
Data.SetOrigin(self.GetOrigin())
Data.AllocateScalars(self.GetOutputVTKType(), 1)

read_data = reader.GetOutput()
read_data.SetExtent(extent)


Data.CopyAndCastFrom(read_data, extent)
outData.ShallowCopy(Data)

return 1
except Exception as e:
print("Exception", e)
raise Exception(e)
logger.error(e)
finally:
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
return 1
if os.path.exists(rawfname):
del reader
logger.info("Removing temporary file: {}".format(rawfname))
os.remove(rawfname)


class cilRawCroppedReader(cilBaseCroppedReader, cilRawReaderInterface):
Expand Down

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