Hi everyone! I’m trying to open a .log document on SkyScanReconImport module but when I try it it doesn’t work. On the python console appear some annotations (photo attached) but I don’t understand what does it mean.
If anyone knows where is the problem and can help me I will be so grateful!!!
It is possible that the log format has changed since we implemented this function. Can you share your *rec.log file and the tiff stack so that we can try to reproduce this error on our end.
Also next time, please tag this question as SlicerMorph as shown below.
This is a common error when reading text files with unknown encoding. To fix the error, specify encoding (if you know that the log files contain special characters encoded as utf-8 then use that, otherwise you can use latin1) when you open the file.
Is there a way to know this without prior knowledge? Or rather is there an issue trying to read everything with UTF-8 encoding?
If encoding is not specified by the software developer and not included in the file format then you can only guess.
If you know that the encoding is utf-8 then use that. If you don’t have information then it is safe to use latin1, because not all byte sequences are valid utf-8 but everything is valid latin1. You may also use chardet that tries to guess the most probable encoding.
This is the latest version of the log file that I can get my hands onto. There is no format specification I can see of. Application that creates this is windows only. So perhaps UTF-8 will be fine?
[System]
Scanner=SkyScan1275
Instrument S/N=001
Software Version=1.0.16
Embedded Controller Version=3.5
Home Directory=C:\SkyScan1275
Source Type=Hamamatsu L11871
Camera Type=DEXELA1512
Camera Pixel Size (um)=75.0
Camera X/Y Ratio=1.0000
[User]
User Name=SkyScan
Computer Name=SCAN1275_001
[Acquisition]
Data Directory=D:\Results\kjell\2017-144_embryo Ali\1275_embryo_7um_
Filename Prefix=1275_embryo_7um_~00
Number Of Files= 601
Number Of Rows= 1536
Number Of Columns= 1944
Filename Index Length=8
Partial Width=OFF
Image crop origin X=0
Image crop origin Y=0
Camera binning=1x1
Image Rotation=-0.03800
Optical Axis (line)= 760
Object to Source (mm)=24.755
Camera to Source (mm)=286.0
Source Voltage (kV)= 80
Source Current (uA)= 124
Image Pixel Size (um)=7.000817
Scaled Image Pixel Size (um)=7.000817
Image Format=TIFF
Depth (bits)=16
Reference Intensity=58000
Exposure (ms)=57
Rotation Step (deg)=0.600
Use 360 Rotation=YES
Scanning position=13.965 mm
Frame Averaging=ON (4)
Random Movement=OFF (30)
Flat Field Correction=ON
FF updating interval=120
Filter=Al 1mm
Gantry direction=CC
Rotation Direction=CC
Scanning Start Angle=0.000
Type of Detector Motion=STEP AND SHOOT
Scanning Trajectory=ROUND
Number Of Horizontal Offset Positions=1
Suggested HU - Calibration=180000
Number of connected scans=2
Current scan number=1
Number of lines to be reconstructed=864
Study Date and Time=22 Sep 2017 06h:56m:05s
Scan duration=0h:12m:25s
Maximum vertical TS=5.0
[Reconstruction]
Reconstruction Program=NRecon
Program Version=Version: 1.7.1.2
Program Home Directory=C:\SkyScan1275
Reconstruction engine=GPUReconServer
Engine version=Version: 1.7.1
Reconstruction from batch=No
Postalignment=-1.00
Connected Reconstruction (parts)=2
Sub-scan post alignment [0]=-2.000000
Sub-scan post alignment [1]=-1.000000
Sub-scan scan length [0]=853
Sub-scan scan length [1]=864
Used extra rotation per scan(deg)= 0.000 0.000
Used extra shift in X per scan(micron)= 0.000 -3.060
Used extra shift in Y per scan(micron)= 0.000 8.976
Reconstruction servers= SCAN1275_001
Dataset Origin=SkyScan1275
Dataset Prefix=1275_embryo_7um_~01
Dataset Directory=D:\Results\kjell\2017-144_embryo Ali\1275_embryo_7um_
Output Directory=D:\Results\kjell\2017-144_embryo Ali\1275_embryo_7um_\1275_embryo_7um_Rec
Time and Date=Sep 22, 2017 07:42:56
First Section=421
Last Section=2050
Reconstruction duration per slice (seconds)=0.381733
Total reconstruction time (854 slices) in seconds=326.000000
Section to Section Step=1
Sections Count=1630
Result File Type=BMP
Result File Header Length (bytes)=1134
Result Image Width (pixels)=1108
Result Image Height (pixels)=876
Pixel Size (um)=7.00082
Reconstruction Angular Range (deg)=360.00
Use 180+=OFF
Angular Step (deg)=0.6000
Smoothing=1
Smoothing kernel=2 (Gaussian)
Ring Artifact Correction=6
Draw Scales=OFF
Object Bigger than FOV=OFF
Reconstruction from ROI=ON
ROI Top (pixels)=1471
ROI Bottom (pixels)=593
ROI Left (pixels)=418
ROI Right (pixels)=1529
ROI reference length=1944
Filter cutoff relative to Nyquist frequency=100
Filter type=0
Filter type description=Hamming (Alpha=0.54)
Undersampling factor=1
Threshold for defect pixel mask (%)=0
Beam Hardening Correction (%)=0
CS Static Rotation (deg)=41.43
Minimum for CS to Image Conversion=0.000000
Maximum for CS to Image Conversion=0.080000
HU Calibration=OFF
BMP LUT=0
Cone-beam Angle Horiz.(deg)=30.740322
Cone-beam Angle Vert.(deg)=24.507914
Automatic matching in Z=50
Automatic matching in X/Y=50
Automatic matching in rotation=5.000000
Automatic fusion=1
[File name convention]
Filename Index Length=8
Filename Prefix=1275_embryo_7um__rec
UTF-8 support in Windows is still fairly new (Windows API support was added a couple of years ago and you still need to specify a manifest to indicate that your application uses UTF-8 and not code pages). So, only use UTF-8 if the manufacturer ID the software explicitly told you that they use UTF-8 or your tests indicate this.
You can test by using non-ASCII characters in the Home directory, Data directory, Output directory, Filename prefix, etc. and see how they get encoded in the log file.
Most likely either the current system code page or some hardcoded code page (e.g. Latin1) is used in the file. I would recommend to assume that the log file uses Latin1 encoding, because the worst that can happen is you get some mojibake in a few lines, which you probably don’t use anyway.
How can I make 3Dslicer uses latin1 instead of uft-8 to read the .log file?
I was trying to solve it but I can’t. I send you the .log, maybe this way you can see the problem.
Thank you so much!
[System]
Scanner=SkyScan1278
Instrument S/N=15B14008
Software Version=1.2
Embedded Controller Version=3.5
Home Directory=C:\SkyScan1278
Source Type=RTW MCBM65B-50
Camera Type=DEXELA1512
Camera Pixel Size (um)=75.0
Camera X/Y Ratio=1.0000
[User]
User Name=u0118485
Computer Name=GBW-D-W2599
[Acquisition]
Data Directory=C:\Users\u0118485\Documents\results\Cage 1\pup16_6mU
Filename Prefix=Pup16_6mT_
Number Of Files= 360
Number Of Rows= 1944
Number Of Columns= 860
Filename Index Length=8
Frame Index Length=8
Partial Width= 56%
Image crop origin X=338
Image crop origin Y=0
Camera binning=1x1
Image Rotation=0.01000
Optical Axis (line)= 964
Object to Source (mm)=200.0
Camera to Source (mm)=286.0
Source Voltage (kV)= 54
Source Current (uA)= 701
Image Pixel Size (um)=51.423000
Scaled Image Pixel Size (um)=51.423000
Image Format=TIFF
Depth (bits)=16
Exposure (ms)=80
Rotation Step (deg)=1.000
Use 360 Rotation=YES
Scanning position=72.675 mm
Frame Averaging=ON (2)
Flat Field Correction=ON
Geometrical Correction=ON
Filter=Al 1mm
Gantry direction=CC
Rotation Direction=CC
List mode=OFF (20)
Scanning Start Angle=0
Number Of Horizontal Offset Positions=1
Type of Detector Motion=STEP AND SHOOT
FF updating interval= 60
Scanning Trajectory=ROUND
Number of connected scans=1
Current scan number=1
Number of lines to be reconstructed=0
Study Date and Time=03 Apr 2020 11h:41m:02s
Scan duration=0h:2m:27s
Suggested HU - Calibration=180000
Maximum vertical TS=5.0
[Reconstruction]
Reconstruction Program=NRecon
Program Version=Version: 1.7.3.1
Program Home Directory=C:\Users\labmo\Desktop\Núria\BMD\NReconServerLocal64 (1)
Reconstruction engine=NReconServer
Engine version=Version: 1.7.3
Reconstruction from batch=No
Postalignment Applied=1
Postalignment=0.50
Reconstruction servers= DESKTOP-NK9CDGM
Reconstruction mode=Standard
Dataset Origin=SkyScan1278
Dataset Prefix=Pup16_6mT_
Dataset Directory=C:\Users\labmo\Desktop\Núria\TFG\6 months CT\Cage 1\pup16_6mU
Output Directory=C:\Users\labmo\Desktop\Núria\TFG\6 months CT\Cage 1\pup16_6mU\pup16_resprec
Time and Date=Nov 21, 2022 09:54:51
First Section=244
Last Section=1150
Reconstruction duration per slice (seconds)=0.041896
Total reconstruction time (907 slices) in seconds=38.000000
Section to Section Step=1
Sections Count=907
Result File Type=TIF
Result File Header Length (bytes)=12
Result Image Width (pixels)=596
Result Image Height (pixels)=476
Pixel Size (um)=51.42300
Reconstruction Angular Range (deg)=360.00
Use 180+=OFF
Angular Step (deg)=1.0000
Smoothing=1
Smoothing kernel=2 (Gaussian)
Ring Artifact Correction=2
Draw Scales=OFF
Object Bigger than FOV=OFF
Reconstruction from ROI=ON_ROUND
ROI Top (pixels)=738
ROI Bottom (pixels)=259
ROI Left (pixels)=129
ROI Right (pixels)=726
ROI reference length=860
Filter cutoff relative to Nyquist frequency=100
Filter type=0
Filter type description=Hamming (Alpha=0.54)
Undersampling factor=1
Threshold for defect pixel mask (%)=0
Beam Hardening Correction (%)=10
CS Static Rotation (deg)=0.00
CS Static Rotation Total(deg)=0.00
Minimum for CS to Image Conversion=-0.003000
Maximum for CS to Image Conversion=0.050000
HU Calibration=OFF
BMP LUT=0
Cone-beam Angle Horiz.(deg)=12.617935
Cone-beam Angle Vert.(deg)=28.063406
[File name convention]
Filename Index Length=8
Filename Prefix=Pup16_6mT__rec
@Nuria_Gallego_Fndz I have updated the SkyScanReconImport module with a field to select the log file encoding type. I’m attaching a screenshot below. The updated module can be downloaded from the SlicerMorph Repo or will be available to update from the extension manager tomorrow. It’d be great to know if this solves your issue.
Thank you so much! Now I can open de .log file without problem.
