Report generation flags - galizia-lab/pyview GitHub Wiki
List of Flags
CTV_scalebar
What does it do?
Specifies whether a scalebar is drawn next to an overview/movie frame
Default value: False
What values can it take?
A boolean value (True/False).
Are values expected to be in specific units?
No
Special Notes
None
CTV_firstframe
What does it do?
integer indicating a frame number, where frames are numbered 0, 1, 2.... Used in calculating CTVs
Default value: 22
What values can it take?
Integer values >=0
Are values expected to be in specific units?
No
Special Notes
None
CTV_lastframe
What does it do?
integer indicating a frame number, where frames are numbered 0, 1, 2.... Used in calculating CTVs
Default value: 36
What values can it take?
Integer values >=0
Are values expected to be in specific units?
No
Special Notes
None
CTV_Method
What does it do?
Specifies the method for curve-to-value conversion. See here for more info.
Default value: 22
What values can it take?
A positive integer value , i.e., a value in {1, 2, 3, ..} or a string value. When it is an integer, an internal CTV method will be used. When it is a string, it specifies the name of the custom function to use. The flag CTV_MethodFile specifies the file in which to look for finding this function.
Are values expected to be in specific units?
No
Special Notes
Related flag: CTV_MethodFile
CTV_MethodFile
What does it do?
Specifies file which contains the custom CTV function specified in CTV_Method. Only used when CTV_Method is a string.
Default value: 'not set yet' (which is a not a valid filename)
What values can it take?
A string value. Must point to a valid file on the file system.
Are values expected to be in specific units?
No
Special Notes
Related flag: CTV_Method
Signal_FilterSpaceFlag
What does it do?
Toggles on/off the spatial filter applied to sig1 before generating overview frames or movies
Default value: False
What values can it take?
A boolean value (True/False).
Are values expected to be in specific units?
No
Special Notes
None
Signal_FilterSpaceSize
What does it do?
Specifies the standard deviation of the spatial gaussian filter applied to sig1 before creating overviews/movies. Only used if 'Signal_FilterSpaceFlag' is True
Default value: 3
What values can it take?
A positive integer value
Are values expected to be in specific units?
No
Special Notes
None
Signal_FilterTimeFlag
What does it do?
Toggles on/off the temporal filter applied to sig1 before generating overview frames or movies
Default value: False
What values can it take?
A boolean value (True/False).
Are values expected to be in specific units?
No
Special Notes
None
Signal_FilterTimeSize
What does it do?
Specifies the standard deviation of the temporal gaussian filter applied to sig1 before creating movies. Only used if 'Signal_FilterTimeFlag' is True
Default value: 3
What values can it take?
A positive integer value
Are values expected to be in specific units?
No
Special Notes
None
SO_MV_scalemin
What does it do?
Specifies the lower limit for the data range used when generating overviews or exporting movies
Default value: 0
What values can it take?
Any number
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_MV_scalemax, mv_individualScale, SO_indivdualScale
SO_MV_scalemax
What does it do?
Specifies the upper limit for the data range used when generating overviews or exporting movies
Default value: 1
What values can it take?
Any number
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_MV_scalemin, mv_individualScale, SO_indivdualScale
RM_Radius
What does it do?
Specifies the size of glomeruli read from .coor file, used when marking ROIs on overviews and exporting glodatamixes
Default value: 5
What values can it take?
Integer values greater than 0
Are values expected to be in specific units?
Number of pixels
Special Notes
Related flags: SO_showROIs
RM_ROITrace
What does it do?
Indicates the file from which component masks are sourced
Default value: 3
What values can it take?
- 0 : read the .coor file
- 1 : (not tested) read the .tif file (8-bit, value indicates the name of the glomerulus)
- 2 : read the .Area file (IDL format).
- 3 : read the .roi file created in ILTIS
- 4 : read the .roi.tif file created by a processing pipeline
- 5 : read the .area.tif file created in ILTIS
Where are the masks located?
Information about units (e.g. glomeruli) are in folder STG_OdormaskPath (default: "05_COOR".) Formats are: .roi, .coor (legacy, not always working)
Information about areas (e.g. "what is brain, what is not") are in folder STG_OdorAreaPath (default: "05_AREA"). Before STG_OdorAreaPath was introduced, .area files were in the OdormaskPath folder) Formats are: .Area (IDL legacy); .area.tif.roi; .area.tif
Are values expected to be in specific units?
No
Special Notes
RM_ROIThreshold
What does it do?
When converting spatial footprints of ROIs into binary masks, all pixels above this percentile will be considered to be inside the binary mask
Default value: 75
What values can it take?
Float values between 0 and 100
Are values expected to be in specific units?
No