Opening a compressed Dicom (MONOCHROME2) file in Python - compression

Question

I tried to open a Dicom file which is a compressed version (JPEG 2000 Image Compression).
I used different free software tools as well as Python libraries (pydicom, VTK, OpenCV) to open it, but they were unsuccessful
In pydicom, decompress() adapts the transfer syntax of the data set, but not the Photometric Interpretation
It seems GDCM can also handle compressed versions, but there is no "one-click" solution to install GDCM on Windows [Solved!]
I would appreciate any suggestions on this.
Dicom Tags:
(0008, 0016) SOP Class UID UI:
(0008, 0018) SOP Instance UID UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733359.3844234830
(0008, 0020) Study Date DA: ''
(0008, 0021) Series Date DA: ''
(0008, 0022) Acquisition Date DA: ''
(0008, 002a) Acquisition DateTime DT: ''
(0008, 0030) Study Time TM: '100304'
(0008, 0031) Series Time TM: '100733'
(0008, 0032) Acquisition Time TM: '100733'
(0008, 0050) Accession Number SH: ''
(0008, 0060) Modality CS: ''
(0008, 0070) Manufacturer LO: ''
(0008, 0080) Institution Name LO: ''
(0008, 1010) Station Name SH: ''
(0008, 1030) Study Description LO: ''
(0008, 103e) Series Description LO: 'Model Acquistion'
(0008, 1070) Operators' Name PN: ''
(0008, 1072) Operator Identification Sequence 1 item(s) ----
(0008, 0080) Institution Name LO: ''
---------
(0008, 1090) Manufacturer's Model Name LO: '4000'
(0010, 0010) Patient's Name PN: ''
(0010, 0020) Patient ID LO: ''
(0010, 0021) Issuer of Patient ID LO: ''
(0010, 0030) Patient's Birth Date DA: ''
(0010, 0040) Patient's Sex CS: ''
(0010, 4000) Patient Comments LT: ''
(0018, 0088) Spacing Between Slices DS: "0.0"
(0018, 1000) Device Serial Number LO: '11307'
(0018, 1020) Software Versions LO: '6.5.0.772'
(0018, 1030) Protocol Name LO: ''
(0020, 000d) Study Instance UID UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100304296.3844877810
(0020, 000e) Series Instance UID UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733328.3844960960
(0020, 0010) Study ID SH: '2016072510030428'
(0020, 0011) Series Number IS: "-2147483648"
(0020, 0012) Acquisition Number IS: "0"
(0020, 0013) Instance Number IS: "1"
(0020, 0052) Frame of Reference UID UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733328.3844960960
(0020, 0060) Laterality CS: 'OS'
(0020, 0200) Synchronization Frame of Reference UI: 1.2.276.0.75.2.2.42.114374073191699.20140417175345187.1980128920
(0020, 4000) Image Comments LT: ''
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0008) Number of Frames IS: "2"
(0028, 0010) Rows US: 1024
(0028, 0011) Columns US: 1024
(0028, 0030) Pixel Spacing DS: '0.005865103,0.001955034'
(0028, 0100) Bits Allocated US: 8
(0028, 0101) Bits Stored US: 8
(0028, 0102) High Bit US: 7
(0028, 0103) Pixel Representation US: 1
(0028, 1050) Window Center DS: "29.0"
(0028, 1051) Window Width DS: "210.0"
(0028, 2110) Lossy Image Compression CS: '01'
(0028, 2112) Lossy Image Compression Ratio DS: "10.0"
(0032, 1060) Requested Procedure Description LO: ''
(0040, 0008) Scheduled Protocol Code Sequence 1 item(s) ----
(0008, 0100) Code Value SH: 'SD-E1'
(0008, 0102) Coding Scheme Designator SH: '99CZM'
(0008, 0103) Coding Scheme Version SH: '1.0'
(0008, 0104) Code Meaning LO: 'ALL SCANS'
(0008, 010d) Context Group Extension Creator UID UI: CZM
(0061, 0111) Private tag data UL: 1
(0061, 0113) Private tag data LO: '1'
(0061, 0115) Private tag data LO: ''
(0061, 0117) Private tag data LO: 'SD-E1.xml'
(0061, 0119) Private tag data LO: 'False'
(0061, 011b) Private tag data LO: ''
(0061, 011d) Private tag data LO: 'True'
---------
(0040, 0244) Performed Procedure Step Start Date DA: ''
(0040, 0245) Performed Procedure Step Start Time TM: '100733'
(0040, 0260) Performed Protocol Code Sequence 1 item(s) ----
(0008, 0100) Code Value SH: 'SD-S2'
(0008, 0102) Coding Scheme Designator SH: ''
(0008, 0103) Coding Scheme Version SH: '1.0'
(0008, 0104) Code Meaning LO: 'Macular Cube 512x128'
(0008, 010d) Context Group Extension Creator UID UI: CZM
(0061, 0111) Private tag data UL: 2
(0061, 0113) Private tag data LO: '1'
(0061, 0115) Private tag data LO: ''
(0061, 0117) Private tag data LO: 'SD-S2.xml'
(0061, 0119) Private tag data LO: 'False'
(0061, 011b) Private tag data LO: 'No Hires in center.No parameters can be modified.'
(0061, 011d) Private tag data LO: 'False'
---------
(0040, 1001) Requested Procedure ID SH: ''
(0057, 0001) Private Creator UI: 1.2.276.0.75.2.2.42.7
(0057, 1003) Private tag data UL: 1
(0057, 1015) Private tag data LO: 'CZMI'
(0057, 1021) Private tag data LO: ''
(0057, 1023) Private tag data LO: '116525681374'
(0059, 1000) Private tag data LO: 'DATAFILES/E039/3RT8Q85TM1Y7VT7X31WNLNBV99GA43BOJ27IOLS4X2ZU.EX.DCM'
(0059, 1005) Private tag data SL: 0
(0059, 3500) Private tag data SL: 1
(0063, 1000) Private tag data FL: 0.0
(0063, 1005) Private tag data FL: 6.0
(0063, 1010) Private tag data FL: 2.0
(0063, 1015) Private tag data FL: -64.0
(0063, 1020) Private tag data UL: 141
(0063, 1025) Private tag data FL: 0.0
(0063, 1026) Private tag data FL: 0.0
(0063, 1030) Private tag data FL: 1.0
(0063, 1032) Private tag data FL: 1.0
(0063, 1035) Private tag data SL: 113
(0063, 1047) Private tag data FL: 297.0
(0063, 1048) Private tag data FL: 872.0
(0063, 1049) Private tag data FL: 1222.0
(0071, 1070) Private tag data FL: -292.0
(0071, 1095) Private tag data FL: 0.0
(0071, 1100) Private tag data FL: 0.0
(0071, 1105) Private tag data SL: 0
(0073, 1085) Private tag data FL: 1.0
(0073, 1090) Private tag data SL: 0
(0073, 1095) Private tag data SL: 0
(0073, 1100) Private tag data SL: 0
(0073, 1105) Private tag data FL: 0.0
(0073, 1110) Private tag data FL: 0.0
(0073, 1125) Private tag data SL: Array of 128 elements
(0073, 1135) Private tag data FL: 0.6000000238418579
(0073, 1200) Private tag data SL: Array of 128 elements
(0075, 1015) Private tag data 0 item(s) ----
(0075, 1020) Private tag data SL: 0
(0075, 1021) Private tag data SL: 0
(0075, 1035) Private tag data FL: 3.5299999713897705
(0075, 1065) Private tag data FL: 0.0
(0075, 1070) Private tag data FL: 0.0
(0075, 1075) Private tag data FL: 0.0
(0075, 1080) Private tag data FL: 0.0
(0075, 1085) Private tag data SL: 0
(0075, 1210) Private tag data UL: 0
(0075, 1215) Private tag data FL: -inf
(0075, 1220) Private tag data FL: -inf
(7fe0, 0010) Pixel Data OB: Array of 211106 elements ```

Answer 1

I've determined how to unscramble these obfuscated CZM DICOM datasets. Essentially CZM transposes three regions of the JPEG 2000 data and then overwrites those by XORing every 7th byte with 0x5A, which is pretty nasty.
The following function should reverse this, producing a normal JPEG 2000 data stream that can then be written to file or opened with Pillow:
import math
def unscramble_czm(frame: bytes) -> bytearray:
"""Return an unscrambled image frame.
Parameters
----------
frame : bytes
The scrambled CZM JPEG 2000 data frame as found in the DICOM dataset.
Returns
-------
bytearray
The unscrambled JPEG 2000 data.
"""
# Fix the 0x5A XORing
frame = bytearray(frame)
for ii in range(0, len(frame), 7):
frame[ii] = frame[ii] ^ 0x5A
# Offset to the start of the JP2 header - empirically determined
jp2_offset = math.floor(len(frame) / 5 * 3)
# Double check that our empirically determined jp2_offset is correct
offset = frame.find(b"\x00\x00\x00\x0C")
if offset == -1:
raise ValueError("No JP2 header found in the scrambled pixel data")
try:
assert jp2_offset == offset
except AssertionError:
raise ValueError(
f"JP2 header found at offset {offset} rather than the expected "
f"{jp2_offset}"
)
d = bytearray()
d.extend(frame[jp2_offset:jp2_offset + 253])
d.extend(frame[993:1016])
d.extend(frame[276:763])
d.extend(frame[23:276])
d.extend(frame[1016:jp2_offset])
d.extend(frame[:23])
d.extend(frame[763:993])
d.extend(frame[jp2_offset + 253:])
assert len(d) == len(frame)
return d