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In [268]:



    


%pylab inline

import io3d
from pathlib import Path



    


















    






Populating the interactive namespace from numpy and matplotlib

Virtual hepatectomy

Merge manual segmentation of left liver with ircad segmentation of the liver. Input data:

  • Manual segmentation of left part of the liver with careful segmentation of resection line but no care about the segmentation quality on the liver boundary.

  • Manual liver segmentation from ircad

In the fallowing scrip we just combine both this sources into one file with labeling of left and right part of the liver.





In [269]:



    


# 6, 11, 16 nefunguje
ircad_id = "10"
ircad_id = "12"
ircad_id = "11"
ircad_id = "20"



    











In [270]:



    


pth_left = f"C:/Users/Jirik/lisa_data/ircad{ircad_id}_left.pklz"
pth_left = f"G:\Můj disk\data\medical\orig\ircad_left_right/patient_dicom_seg{ircad_id}.pklz"
pth_liver = f"C:/Users/Jirik/data/medical/orig/3Dircadb1.{ircad_id}/MASKS_DICOM/liver/"
pth_output = f"C:/Users/Jirik/lisa_data/ircad{ircad_id}_liver_LR.pklz"



    











In [271]:



    


dp_left = io3d.read(pth_left, dataplus_format=True)
dp_liver = io3d.read(pth_liver, dataplus_format=True)
imshow(dp_left["data3d"][30,:,:])



    


















    






2020-05-26 14:19:44.142 | DEBUG    | io3d.datareader:Get3DData:146 - file read recognized
2020-05-26 14:19:44.144 | DEBUG    | io3d.datareader:__ReadFromFile:254 - pklz format detected
2020-05-26 14:19:45.050 | DEBUG    | io3d.datareader:Get3DData:166 - dataplus format
2020-05-26 14:19:45.054 | DEBUG    | io3d.datareader:Get3DData:170 - datap keys () : dict_keys(['series_number', 'datadir', 'voxelsize_mm', 'data3d'])
2020-05-26 14:19:45.065 | DEBUG    | io3d.datareader:Get3DData:150 - directory read recognized
2020-05-26 14:19:45.084 | WARNING  | io3d.dcmreaddata:is_dicom_dir:74 - Unable to read dicom file dicomdir.pkl
2020-05-26 14:19:45.087 | WARNING  | io3d.dcmreaddata:is_dicom_dir:75 - File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.
2020-05-26 14:19:45.096 | DEBUG    | io3d.datareader:__ReadFromDirectory:191 - Dir - DICOM
2020-05-26 14:19:45.097 | DEBUG    | io3d.datareader:__ReadFromDirectory:192 - dicom_expected None
2020-05-26 14:19:45.103 | INFO     | io3d.misc:read_pkl_and_pklz:115 - Input gzip exception: Not a gzipped file (b'\x80\x04')
2020-05-26 14:19:45.107 | DEBUG    | io3d.dcmreaddata:get_sorted_series_files:808 - SeriesNumber: None
2020-05-26 14:19:45.132 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_0
2020-05-26 14:19:45.140 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_1
2020-05-26 14:19:45.154 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_2
2020-05-26 14:19:45.166 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_3
2020-05-26 14:19:45.182 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_4
2020-05-26 14:19:45.196 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_5
2020-05-26 14:19:45.208 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_6
2020-05-26 14:19:45.220 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_7
2020-05-26 14:19:45.230 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_8
2020-05-26 14:19:45.244 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_9
2020-05-26 14:19:45.257 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_10
2020-05-26 14:19:45.271 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_11
2020-05-26 14:19:45.286 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_12
2020-05-26 14:19:45.302 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_13
2020-05-26 14:19:45.309 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_14
2020-05-26 14:19:45.320 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_15
2020-05-26 14:19:45.331 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_16
2020-05-26 14:19:45.344 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_17
2020-05-26 14:19:45.367 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_18
2020-05-26 14:19:45.377 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_19
2020-05-26 14:19:45.389 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_20
2020-05-26 14:19:45.398 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_21
2020-05-26 14:19:45.409 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_22
2020-05-26 14:19:45.422 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_23
2020-05-26 14:19:45.431 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_24
2020-05-26 14:19:45.441 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_25
2020-05-26 14:19:45.458 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_26
2020-05-26 14:19:45.470 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_27
2020-05-26 14:19:45.481 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_28
2020-05-26 14:19:45.494 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_29
2020-05-26 14:19:45.507 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_30
2020-05-26 14:19:45.520 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_31
2020-05-26 14:19:45.529 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_32
2020-05-26 14:19:45.542 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_33
2020-05-26 14:19:45.552 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_34
2020-05-26 14:19:45.561 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_35
2020-05-26 14:19:45.571 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_36
2020-05-26 14:19:45.580 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_37
2020-05-26 14:19:45.592 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_38
2020-05-26 14:19:45.620 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_39
2020-05-26 14:19:45.630 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_40
2020-05-26 14:19:45.641 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_41
2020-05-26 14:19:45.652 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_42
2020-05-26 14:19:45.661 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_43
2020-05-26 14:19:45.671 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_44
2020-05-26 14:19:45.681 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_45
2020-05-26 14:19:45.691 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_46
2020-05-26 14:19:45.698 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_47
2020-05-26 14:19:45.708 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_48
2020-05-26 14:19:45.720 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_49
2020-05-26 14:19:45.729 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_50
2020-05-26 14:19:45.739 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_51
2020-05-26 14:19:45.748 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_52
2020-05-26 14:19:45.758 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_53
2020-05-26 14:19:45.771 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_54
2020-05-26 14:19:45.779 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_55
2020-05-26 14:19:45.790 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_56
2020-05-26 14:19:45.796 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_57
2020-05-26 14:19:45.805 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_58
2020-05-26 14:19:45.812 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_59
2020-05-26 14:19:45.823 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_60
2020-05-26 14:19:45.829 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_61
2020-05-26 14:19:45.838 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_62
2020-05-26 14:19:45.847 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_63
2020-05-26 14:19:45.863 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_64
2020-05-26 14:19:45.873 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_65
2020-05-26 14:19:45.882 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_66
2020-05-26 14:19:45.894 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_67
2020-05-26 14:19:45.902 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_68
2020-05-26 14:19:45.910 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_69
2020-05-26 14:19:45.922 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_70
2020-05-26 14:19:45.928 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_71
2020-05-26 14:19:45.935 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_72
2020-05-26 14:19:45.943 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_73
2020-05-26 14:19:45.955 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_74
2020-05-26 14:19:45.962 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_75
2020-05-26 14:19:45.970 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_76
2020-05-26 14:19:45.976 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_77
2020-05-26 14:19:45.985 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_78
2020-05-26 14:19:45.992 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_79
2020-05-26 14:19:46.001 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_80
2020-05-26 14:19:46.005 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_81
2020-05-26 14:19:46.013 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_82
2020-05-26 14:19:46.022 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_83
2020-05-26 14:19:46.034 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_84
2020-05-26 14:19:46.044 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_85
2020-05-26 14:19:46.055 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_86
2020-05-26 14:19:46.063 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_87
2020-05-26 14:19:46.072 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_88
2020-05-26 14:19:46.078 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_89
2020-05-26 14:19:46.089 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_90
2020-05-26 14:19:46.094 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_91
2020-05-26 14:19:46.104 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_92
2020-05-26 14:19:46.113 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_93
2020-05-26 14:19:46.121 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_94
2020-05-26 14:19:46.127 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_95
2020-05-26 14:19:46.134 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_96
2020-05-26 14:19:46.140 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_97
2020-05-26 14:19:46.145 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_98
2020-05-26 14:19:46.155 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_99
2020-05-26 14:19:46.163 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_100
2020-05-26 14:19:46.172 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_101
2020-05-26 14:19:46.178 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_102
2020-05-26 14:19:46.188 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_103
2020-05-26 14:19:46.193 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_104
2020-05-26 14:19:46.200 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_105
2020-05-26 14:19:46.208 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_106
2020-05-26 14:19:46.213 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_107
2020-05-26 14:19:46.224 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_108
2020-05-26 14:19:46.230 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_109
2020-05-26 14:19:46.239 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_110
2020-05-26 14:19:46.244 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_111
2020-05-26 14:19:46.254 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_112
2020-05-26 14:19:46.259 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_113
2020-05-26 14:19:46.265 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_114
2020-05-26 14:19:46.275 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_115
2020-05-26 14:19:46.282 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_116
2020-05-26 14:19:46.292 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_117
2020-05-26 14:19:46.299 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_118
2020-05-26 14:19:46.309 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_119
2020-05-26 14:19:46.318 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_120
2020-05-26 14:19:46.325 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_121
2020-05-26 14:19:46.331 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_122
2020-05-26 14:19:46.338 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_123
2020-05-26 14:19:46.343 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_124
2020-05-26 14:19:46.351 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_125
2020-05-26 14:19:46.358 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_126
2020-05-26 14:19:46.364 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_127
2020-05-26 14:19:46.373 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_128
2020-05-26 14:19:46.380 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_129
2020-05-26 14:19:46.390 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_130
2020-05-26 14:19:46.396 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_131
2020-05-26 14:19:46.404 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_132
2020-05-26 14:19:46.414 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_133
2020-05-26 14:19:46.425 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_134
2020-05-26 14:19:46.433 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_135
2020-05-26 14:19:46.439 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_136
2020-05-26 14:19:46.446 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_137
2020-05-26 14:19:46.457 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_138
2020-05-26 14:19:46.468 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_139
2020-05-26 14:19:46.479 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_140
2020-05-26 14:19:46.491 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_141
2020-05-26 14:19:46.496 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_142
2020-05-26 14:19:46.504 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_143
2020-05-26 14:19:46.511 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_144
2020-05-26 14:19:46.519 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_145
2020-05-26 14:19:46.526 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_146
2020-05-26 14:19:46.536 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_147
2020-05-26 14:19:46.542 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_148
2020-05-26 14:19:46.547 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_149
2020-05-26 14:19:46.557 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_150
2020-05-26 14:19:46.563 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_151
2020-05-26 14:19:46.573 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_152
2020-05-26 14:19:46.578 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_153
2020-05-26 14:19:46.588 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_154
2020-05-26 14:19:46.594 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_155
2020-05-26 14:19:46.603 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_156
2020-05-26 14:19:46.610 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_157
2020-05-26 14:19:46.619 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_158
2020-05-26 14:19:46.626 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_159
2020-05-26 14:19:46.637 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_160
2020-05-26 14:19:46.642 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_161
2020-05-26 14:19:46.648 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_162
2020-05-26 14:19:46.657 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_163
2020-05-26 14:19:46.662 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_164
2020-05-26 14:19:46.671 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_165
2020-05-26 14:19:46.677 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_166
2020-05-26 14:19:46.692 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_167
2020-05-26 14:19:46.702 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_168
2020-05-26 14:19:46.707 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_169
2020-05-26 14:19:46.713 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_170
2020-05-26 14:19:46.721 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_171
2020-05-26 14:19:46.727 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_172
2020-05-26 14:19:46.736 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_173
2020-05-26 14:19:46.743 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_174
2020-05-26 14:19:46.755 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_175
2020-05-26 14:19:46.762 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_176
2020-05-26 14:19:46.770 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_177
2020-05-26 14:19:46.779 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_178
2020-05-26 14:19:46.790 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_179
2020-05-26 14:19:46.798 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_180
2020-05-26 14:19:46.806 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_181
2020-05-26 14:19:46.821 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_182
2020-05-26 14:19:46.827 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_183
2020-05-26 14:19:46.835 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_184
2020-05-26 14:19:46.843 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_185
2020-05-26 14:19:46.848 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_186
2020-05-26 14:19:46.857 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_187
2020-05-26 14:19:46.865 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_188
2020-05-26 14:19:46.876 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_189
2020-05-26 14:19:46.885 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_190
2020-05-26 14:19:46.892 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_191
2020-05-26 14:19:46.899 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_192
2020-05-26 14:19:46.909 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_193
2020-05-26 14:19:46.918 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_194
2020-05-26 14:19:46.927 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_195
2020-05-26 14:19:46.938 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_196
2020-05-26 14:19:46.943 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_197
2020-05-26 14:19:46.949 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_198
2020-05-26 14:19:46.960 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_199
2020-05-26 14:19:46.970 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_200
2020-05-26 14:19:46.977 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_201
2020-05-26 14:19:46.987 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_202
2020-05-26 14:19:46.992 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_203
2020-05-26 14:19:46.999 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_204
2020-05-26 14:19:47.009 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_205
2020-05-26 14:19:47.017 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_206
2020-05-26 14:19:47.028 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_207
2020-05-26 14:19:47.043 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_208
2020-05-26 14:19:47.052 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_209
2020-05-26 14:19:47.060 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_210
2020-05-26 14:19:47.066 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_211
2020-05-26 14:19:47.075 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_212
2020-05-26 14:19:47.083 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_213
2020-05-26 14:19:47.092 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_214
2020-05-26 14:19:47.100 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_215
2020-05-26 14:19:47.108 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_216
2020-05-26 14:19:47.115 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_217
2020-05-26 14:19:47.125 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_218
2020-05-26 14:19:47.132 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_219
2020-05-26 14:19:47.140 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_220
2020-05-26 14:19:47.147 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_221
2020-05-26 14:19:47.156 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_222
2020-05-26 14:19:47.165 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_223
2020-05-26 14:19:47.176 | DEBUG    | io3d.dcmreaddata:get_3Ddata:334 - Data size: 58982400, shape: (512, 512)x225 file C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_224
2020-05-26 14:19:47.565 | DEBUG    | io3d.dcmreaddata:get_metaData:529 - Filename: C:\Users\Jirik\data\medical\orig\3Dircadb1.20\MASKS_DICOM\liver\image_0
2020-05-26 14:19:47.583 | DEBUG    | io3d.dcmreaddata:get_slice_location:917 - Estimating SliceLocation wiht image number and SliceThickness
2020-05-26 14:19:47.587 | DEBUG    | io3d.dcmreaddata:get_slice_location:917 - Estimating SliceLocation wiht image number and SliceThickness
2020-05-26 14:19:47.595 | DEBUG    | io3d.dcmreaddata:get_slice_location:917 - Estimating SliceLocation wiht image number and SliceThickness
2020-05-26 14:19:47.599 | DEBUG    | io3d.dcmreaddata:get_slice_location:917 - Estimating SliceLocation wiht image number and SliceThickness
2020-05-26 14:19:47.603 | INFO     | io3d.dcmreaddata:get_metaData:580 - Problem with tag SeriesDescription, SeriesNumber: 
2020-05-26 14:19:47.607 | INFO     | io3d.dcmreaddata:get_metaData:585 - Problem with tag ImageComments
2020-05-26 14:19:47.894 | DEBUG    | io3d.datareader:Get3DData:166 - dataplus format
2020-05-26 14:19:47.897 | DEBUG    | io3d.datareader:Get3DData:170 - datap keys () : dict_keys(['voxelsize_mm', 'Modality', 'SeriesNumber', 'AcquisitionDate', 'StudyDate', 'StudyID', 'PatientSex', 'PatientID', 'PatientName', 'dcmfilelist', 'series_number', 'datadir', 'data3d'])










    
Out[271]:








<matplotlib.image.AxesImage at 0x1d3031db780>










    
























In [272]:



    


# mask_ll = dp_left["segmentation"] == dp_left["slab"]["left_liver"]
mask_ll = dp_left["data3d"] > 0
imshow(mask_ll[30])
# plt.colorbar()



    


















    
Out[272]:








<matplotlib.image.AxesImage at 0x1d303235668>










    
























In [273]:



    


mask_li = dp_liver["data3d"] > 0
print(np.unique(dp_liver["data3d"]))
imshow(mask_li[20])
# plt.colorbar()



    


















    






[0 1]










    
Out[273]:








<matplotlib.image.AxesImage at 0x1d3034d4a90>










    
























In [274]:



    


mask_ll_li = mask_li & mask_ll
imshow(mask_ll_li[20])



    


















    
Out[274]:








<matplotlib.image.AxesImage at 0x1d3035346d8>










    
























In [275]:



    


dp_liver["data3d"][dp_liver["data3d"] == 1] = 255
dp_liver["data3d"][mask_ll_li] = 128
imshow(dp_liver["data3d"][30])



    


















    
Out[275]:








<matplotlib.image.AxesImage at 0x1d30358dfd0>

Are there both labels?





In [276]:



    


print(np.unique(dp_liver["data3d"]))



    


















    






[  0 128 255]

















In [277]:



    


help(io3d.write)



    


















    






Help on function write in module io3d.datawriter:

write(data3d, path, filetype='auto', metadata=None)
    :param data3d: input ndarray
    :param path: output path, if braces are in the name ("dir/file{:04d}.dcm"), image stack is produced .
    Check function filename_format() for more details.
    :param filetype: dcm, png, h5, ... "image_stack"
    :param metadata: metadata f.e. {'voxelsize_mm': [3,2,2]}
    :return:


















In [278]:



    


# fn = "ircad10.pklz"
io3d.write(dp_liver["data3d"], pth_output, metadata={"voxelsize_mm":dp_liver["voxelsize_mm"]})

Check by read





In [279]:



    


dap = io3d.read(pth_output, dataplus_format=True)

imshow(dap["data3d"][30])



    


















    






2020-05-26 14:19:56.527 | DEBUG    | io3d.datareader:Get3DData:146 - file read recognized
2020-05-26 14:19:56.531 | DEBUG    | io3d.datareader:__ReadFromFile:254 - pklz format detected
2020-05-26 14:19:57.772 | DEBUG    | io3d.datareader:Get3DData:166 - dataplus format
2020-05-26 14:19:57.775 | DEBUG    | io3d.datareader:Get3DData:170 - datap keys () : dict_keys(['series_number', 'datadir', 'voxelsize_mm', 'data3d'])










    
Out[279]:








<matplotlib.image.AxesImage at 0x1d3035f3828>










    
























In [280]:



    


max(0,4)



    


















    
Out[280]:








4

Content source: mjirik/lisa

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