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improvment of the cellvizio reader: reading meta informations from hexcode directly #150

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Merged
maubreville merged 6 commits into from
Feb 5, 2026
+78 −17
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improvment of the cellvizio reader: reading meta informations from hexcode directly #150

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f81612a
improvment cellvizio reader: reading meta informations from hexcode d…
stabiloSlin Feb 5, 2026
1098f94
Update exact/util/cellvizio.py
maubreville Feb 5, 2026
bc332f7
Update exact/util/cellvizio.py
maubreville Feb 5, 2026
c1be0f3
Update exact/util/cellvizio.py
maubreville Feb 5, 2026
797b2e7
Update exact/util/cellvizio.py
maubreville Feb 5, 2026
abbe918
Update exact/util/cellvizio.py
maubreville Feb 5, 2026
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86 changes: 69 additions & 17 deletions exact/util/cellvizio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,36 +52,35 @@ def __init__(self,filename):
self.fi = fileinfo()
self.fileHandle = open(filename, 'rb');
self.fileHandle.seek(5) # we find the FPS at position 05
fFPSByte = self.fileHandle.read(4)
self.fps = struct.unpack('>f', fFPSByte)[0]


# fFPSByte = self.fileHandle.read(4)
# self.fps = struct.unpack('>f', fFPSByte)[0]
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self.fileHandle.seek(10) # we find the image size at position 10
fSizeByte = self.fileHandle.read(4)
self.fi.size = int.from_bytes(fSizeByte, byteorder='big', signed=True)
self.fi.nImages=1000

self.fi.width = 576
if ((self.fi.size/(2*self.fi.width))%2!=0):
self.fi.width=512
self.fi.height=int(self.fi.size/(2*self.fi.width))
else:
self.fi.height=int(self.fi.size/(2*self.fi.width))

self.filestats = stat(self.fileName)
self.fi.nImages=1000
self.fi.nImages = int((self.filestats.st_size-self.fi.offset) / (self.fi.size+self.fi.gapBetweenImages))

self.numberOfFrames = self.fi.nImages


meta = self.getMostRelevantMetaInfo()
self.fi.width = int(meta.get('width', 0))
self.fi.height = int(meta.get('height', 0))
self.fps = float(meta.get('framerate', 0))

self.geometry_imsize = [self.fi.height, self.fi.width]
self.imsize = [self.fi.height, self.fi.width]
self.geometry_tilesize = [(self.fi.height, self.fi.width)]
self.geometry_rows = [1]
self.geometry_columns = [1]
self.levels = [1]
self.channels = 1
self.mpp_x = 250/576 # approximate number for gastroflex, 250 ym field of view, 576 px
self.mpp_y = 250/576

self.fovx = float(meta.get('fovx', 250))
self.fovy = float(meta.get('fovy', 250))
print(f"fovx: {self.fovx}, fovy: {self.fovy}")
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This print statement should be removed or replaced with proper logging. Use logger.debug() instead for debug output in production code.

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Correct, let's do this with the next commit.

self.mpp_x = self.fovx/self.fi.width # approximate number for gastroflex, 250 ym field of view, 576 px
self.mpp_y = self.fovy/self.fi.height
Comment on lines +79 to +80
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Potential division by zero if width or height metadata is missing or zero. The mpp_x and mpp_y calculations will fail if self.fi.width or self.fi.height is 0 (which would happen if the metadata keys are not found, since the default is 0). Add validation to ensure width and height are non-zero before performing these calculations, or provide sensible fallback values.

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# generate circular mask for this file
self.circMask = circularMask(self.fi.width,self.fi.height, self.fi.width-2).mask
Expand All @@ -91,6 +90,44 @@ def __init__(self,filename):
openslide.PROPERTY_NAME_MPP_Y: self.mpp_y,
openslide.PROPERTY_NAME_OBJECTIVE_POWER:20,
openslide.PROPERTY_NAME_VENDOR: 'MKT'}


def getMetaInfo(self):
# the meta information at the MKT file always starts with "00616C6C 6F776564 5F656761 696E5F65 6F666673 65745F70 61697273 3D" or allowed_egain_eoffset_pairs= in the hex code
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The comment refers to "00616C6C 6F776564 5F656761 696E5F65 6F666673 65745F70 61697273 3D" as the hex representation of "allowed_egain_eoffset_pairs=", but this hex string representation is not actually used in the code and adds unnecessary complexity to the comment. The comment would be clearer if it simply stated that metadata starts with "allowed_egain_eoffset_pairs=".

Suggested change
# the meta information at the MKT file always starts with "00616C6C 6F776564 5F656761 696E5F65 6F666673 65745F70 61697273 3D" or allowed_egain_eoffset_pairs= in the hex code
# the meta information in the MKT file always starts with "allowed_egain_eoffset_pairs="

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self.fileHandle = open(self.fileName, 'rb');
# we need to read the whole file to find the meta information
fileContent = self.fileHandle.read()
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# find start position with fileContent.find(b'allowed_egain_eoffset_pairs=') that searches for the byte sequence
metaStart = fileContent.rfind(b'allowed_egain_eoffset_pairs=')
metaEnd = fileContent.find(b'<CEND', metaStart)
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
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If the '<CEND' marker is not found, find() will return -1, resulting in an incorrect slice that includes content from the start position to near the beginning of the file. Add validation to check if metaEnd is -1 and handle this case appropriately.

Suggested change
metaStart = fileContent.rfind(b'allowed_egain_eoffset_pairs=')
metaEnd = fileContent.find(b'<CEND', metaStart)
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
metaStart = fileContent.rfind(b'allowed_egain_eoffset_pairs=')
if metaStart == -1:
# expected metadata start marker not found
self.fileHandle.close()
print("Meta information start marker 'allowed_egain_eoffset_pairs=' not found.")
return ""
metaEnd = fileContent.find(b'<CEND', metaStart)
if metaEnd == -1:
# expected metadata end marker not found
self.fileHandle.close()
print("Meta information end marker '<CEND' not found.")
return ""
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
self.fileHandle.close()

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The decode operation assumes UTF-8 encoding but provides no error handling if the metadata contains invalid UTF-8 sequences. Consider adding error handling with errors='ignore' or errors='replace' parameter, or catching UnicodeDecodeError to handle corrupted metadata gracefully.

Suggested change
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8', errors='replace')

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print(f"Meta information found: ")
print(metaInfo)
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There's no error handling if the metadata marker is not found. If rfind() returns -1 (not found), the subsequent find() and slice operations will produce incorrect results. Add validation to check if metaStart is -1 and handle this case appropriately, potentially falling back to default values or raising a meaningful error.

Suggested change
metaStart = fileContent.rfind(b'allowed_egain_eoffset_pairs=')
metaEnd = fileContent.find(b'<CEND', metaStart)
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
print(f"Meta information found: ")
print(metaInfo)
metaStart = fileContent.rfind(b'allowed_egain_eoffset_pairs=')
if metaStart == -1:
# metadata marker not found; return empty meta info to avoid invalid slicing
print("Meta information marker 'allowed_egain_eoffset_pairs=' not found in file.")
self.fileHandle.close()
return ""
metaEnd = fileContent.find(b'<CEND', metaStart)
if metaEnd == -1 or metaEnd <= metaStart:
# end marker not found or invalid; return empty meta info to avoid invalid slicing
print("Meta information end marker '<CEND' not found or invalid in file.")
self.fileHandle.close()
return ""
metaInfo = fileContent[metaStart:metaEnd].decode('utf-8')
print(f"Meta information found: ")
print(metaInfo)
self.fileHandle.close()

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return metaInfo

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def getMostRelevantMetaInfo(self):
metaInfo = self.getMetaInfo()
relevantInfo = {}

for line in metaInfo.split('\n'):
if "=" not in line:
continue
key, value = line.split('=')
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The split logic is fragile and will fail if a line contains multiple '=' characters. For example, a line like "key=value=something" would be incorrectly parsed. Consider using split('=', 1) to split only on the first occurrence of '=', or use a more robust parsing approach.

Suggested change
key, value = line.split('=')
key, value = line.split('=', 1)

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if key == 'framerate':
relevantInfo['framerate'] = value
relevantInfo['duration_seconds'] = self.fi.nImages / float(relevantInfo['framerate'])
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elif key == 'width':
relevantInfo['width'] = value
elif key == 'height':
relevantInfo['height'] = value
elif key == 'fovx':
relevantInfo['fovx'] = value
elif key == 'fovy':
relevantInfo['fovy'] = value
elif key == 'patient_id':
relevantInfo['patient_id'] = value
Comment on lines +112 to +134
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The key from the split operation is not stripped of whitespace, which could cause comparison failures if there's any leading or trailing whitespace in the metadata. Consider using key.strip() when comparing against expected key names to make the parsing more robust.

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Generally not a problem in MKT File format.


return relevantInfo

def _2_init__(self, filename):

Expand Down Expand Up @@ -137,7 +174,22 @@ def _2_init__(self, filename):

self.circMask = circularMask(self.fi.width,self.fi.height, self.fi.width-2).mask

@property
def meta_data(self) -> dict:
return self.getMostRelevantMetaInfo()
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@property
def meta_data_dict(self) -> dict:
meta_data_dict = {
'width': 'Image width (pixels)',
'height': 'Image height (pixels)',
'framerate': 'Frame rate (fps)',
'duration_seconds': 'Duration (seconds)',
'patient_id': 'Patient ID',
'fovx': 'Field of view x (micrometers)',
'fovy': 'Field of view y (micrometers)'
}
return meta_data_dict

@property
def seriesInstanceUID(self) -> str:
Expand Down
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