Andrey Fedorov fedorov
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fedorov
/ NUMPY_configure_step_error.txt
Created
January 25, 2013 13:29
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| Running from numpy source directory. | |
| /Users/fedorov/github/Slicer-Superbuild-ITK4-Debug/NUMPY/numpy/distutils/command/config.py:394: DeprecationWarning: | |
| +++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Usage of get_output is deprecated: please do not | |
| use it anymore, and avoid configuration checks | |
| involving running executable on the target machine. | |
| +++++++++++++++++++++++++++++++++++++++++++++++++ | |
| DeprecationWarning) |
fedorov
/ gist:9521408
Created
March 13, 2014 03:18
Example of a DICOM encoding of a mean calculated over a region of interest in CT image, following TID1419
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| (fffe,e000) na (Item with undefined length #=5) # u/l, 1 Item | |
| (0040,a010) CS [CONTAINS] # 8, 1 RelationshipType | |
| (0040,a040) CS [NUM] # 4, 1 ValueType | |
| (0040,a043) SQ (Sequence with undefined length #=1) # u/l, 1 ConceptNameCodeSequence | |
| (fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item | |
| (0008,0100) SH [112031] # 6, 1 CodeValue | |
| (0008,0102) SH [DCM] # 4, 1 CodingSchemeDesignator | |
| (0008,0104) LO [Attenuation Coefficient] # 24, 1 CodeMeaning | |
| (fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem | |
| (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem |
fedorov
/ LabelToDICOMSEGConverterScript.py
Created
February 10, 2015 15:10
Proposed updates for https://github.com/fedorov/Reporting/blob/master/Util/LabelToDICOMSEGConverterScript.py
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| # | |
| # This module was developed by Andrey Fedorov, BWH | |
| # with the support of Slicer Community | |
| # | |
| # This work was supported in part by NIH NCI U01CA151261 grant (Quantitative | |
| # Imaging Network), PI Fiona Fennessy. | |
| # | |
| # This script performs conversion of the segmentation saved as a | |
| # Slicer-readable volume into DICOM SEG format. | |
| # |
fedorov
/ gist:d713971930988dd954dd
Created
March 16, 2015 19:08
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| [fedorov@beat] dcmdump encoded_cases_from_Ethan/QIN_DICOM_test/DICOM/SEG/aorta.dcm | |
| # Dicom-File-Format | |
| # Dicom-Meta-Information-Header | |
| # Used TransferSyntax: Little Endian Explicit | |
| (0002,0000) UL 200 # 4, 1 FileMetaInformationGroupLength | |
| (0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion | |
| (0002,0002) UI =SegmentationStorage # 28, 1 MediaStorageSOPClassUID | |
| (0002,0003) UI [1.2.276.0.7230010.3.1.4.8323329.23367.1426520805.20572] # 54, 1 MediaStorageSOPInstanceUID |
fedorov
/ gist:7f7984dfa7c1cfda8c36
Created
June 16, 2015 13:31
Plus frequency of warnings with settings before June 16, 2015
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| |INFO|486.637000|SERVER> TrackedVideoDevice: Local time offset: 0ms | in PlusServerLauncher(0) | |
| |WARNING|486.638000|SERVER> FanAngles volume reconstructor parameter is deprecated. Use FanAnglesDeg instead (with the same value).; in ..\..\..\PlusLib\src\VolumeReconstruction\vtkVolumeReconstructor.cxx(748) | in PlusServerLauncher(0) | |
| |WARNING|486.639000|SERVER> FanOrigin volume reconstructor parameter is deprecated. Use FanOriginPixels instead (with the same value).; in ..\..\..\PlusLib\src\VolumeReconstruction\vtkVolumeReconstructor.cxx(763) | in PlusServerLauncher(0) | |
| |WARNING|486.640000|SERVER> FanDepth volume reconstructor parameter is deprecated. Use FanRadiusStopPixels instead (with the same value).; in ..\..\..\PlusLib\src\VolumeReconstruction\vtkVolumeReconstructor.cxx(786) | in PlusServerLauncher(0) | |
| |WARNING|486.640000|SERVER> Use of Compounding is deprecated. Use CompoundingMode instead.; in ..\..\..\PlusLib\src\VolumeReconstruction\vtkVolumeReconstructor.cxx(148) | in PlusServerLauncher(0) |
fedorov
/ gist:ff18a2d3d144dcb25531
Created
June 16, 2015 13:33
Warnings frequency with the new settings
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| |INFO|501.924000|SERVER> vtkPlusStartStopRecordingCommand::Execute: StartRecording | in PlusServerLauncher(0) | |
| |WARNING|507.709000|SERVER> Recording of frames takes too long time (0.108sec instead of the allocated 0.1sec). This can cause slow-down of the application and non-uniform sampling. Reduce the acquisition rate or sampling rate to resolve the problem.; in ..\..\..\PlusLib\src\DataCollection\VirtualDevices\vtkVirtualDiscCapture.cxx(323) | in PlusServerLauncher(0) | |
| |WARNING|515.788000|SERVER> Recording of frames takes too long time (0.206sec instead of the allocated 0.1sec). This can cause slow-down of the application and non-uniform sampling. Reduce the acquisition rate or sampling rate to resolve the problem.; in ..\..\..\PlusLib\src\DataCollection\VirtualDevices\vtkVirtualDiscCapture.cxx(323) | in PlusServerLauncher(0) | |
| |WARNING|529.770000|SERVER> Recording of frames takes too long time (0.114sec instead of the allocated 0.1sec). This can cause slow-down of the application and non-uniform sampling. R |
fedorov
/ gist:ef8ac0dcd787e3555b80
Created
June 16, 2015 13:35
Plus capture header file recorded from Slicer PlusRemote
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| ObjectType = Image | |
| NDims = 3 | |
| AnatomicalOrientation = RAI | |
| BinaryData = True | |
| BinaryDataByteOrderMSB = False | |
| CenterOfRotation = 0 0 0 | |
| CompressedData = False | |
| DimSize = 1280 1024 244 | |
| ElementNumberOfChannels = 1 | |
| ElementSpacing = 1 1 1 |
fedorov
/ gist:67ac50a226b56ed12ae7
Created
June 16, 2015 13:36
Plus capture config file - debug low FPS
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| <PlusConfiguration version="2.3" PlusRevision="Plus-2.2.0.4177 - Win32"> | |
| <DataCollection StartupDelaySec="1"> | |
| <DeviceSet Name="BK8818E depth 5.3cm w Slicer post calibration Q" Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)." /> | |
| <Device | |
| Id="TrackerDevice" | |
| Type="Ascension3DG" | |
| AcquisitionRate="50" | |
| LocalTimeOffsetSec="0.15" | |
| FilterAcWideNotch="1" | |
| FilterAcNarrowNotch="0" |
fedorov
/ Config file passed to fCal and Slicer
Created
June 16, 2015 13:47
BWH - debugging Plus low FPS for prostate data acquisition
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| <PlusConfiguration version="2.3" PlusRevision="Plus-2.1.0.3427"> | |
| <DataCollection StartupDelaySec="1"> | |
| <DeviceSet Name="BK8818E depth 5.3cm w Slicer post calibration Q" Description="Epiphan frame grabber with Ascension EM trackers. Sensors in order: Red (111), Green (222), Blue (unmarked)."/> | |
| <Device | |
| Id="TrackerDevice" | |
| Type="Ascension3DG" | |
| AcquisitionRate="50" | |
| LocalTimeOffsetSec="0.15" | |
| FilterAcWideNotch="1" | |
| FilterAcNarrowNotch="0" |
fedorov
/ gist:4f69f0f19da3c2ff0db1
Created
October 21, 2015 01:51
urlopen CERTIFICATE_VERIFY_FAILED error
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| import TCIABrowserLib | |
| c=TCIABrowserLib.TCIAClient(baseUrl='https://services.cancerimagingarchive.net/services/TCIA/TCIA/query') | |
| c.get_collection_values() |
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