Overview flags - galizia-lab/pyview GitHub Wiki
List of flags
SO_bgColor
What does it do?
Indicates the color of border of overviews and tapestries.
Default value: w (white)
What values can it take?
A string value. See here for valid values for colors.
Are values expected to be in specific units?
No
Special Notes
None
SO_cutborder
What does it do?
specifies the number of pixels to exclude on all sides of of the overview frame.
Default value: 0
What values can it take?
A positive integer value.
Are values expected to be in specific units?
No
Special Notes
None
SO_fgColor
What does it do?
Indicates the color of annotations to be added onto to overviews and tapestries.
Default value: k (black)
What values can it take?
A string value. See here for valid values for colors.
Are values expected to be in specific units?
No
Special Notes
None
SO_fontName
What does it do?
Indicates the name of the system font to use when adding colorbar to overviews. E.g.: 'DejeVuSans'. Use 'None' for a default internal font
Default value: None
What values can it take?
A string value. VIEW tries to find a font file with the specified name and either .ttf or .otf extension.
- On Linux, you can open a terminal and issue the command
fc-listto get a list of system font files. - On Windows, you can open
Fonts Settings(Control Panel->Personalization->Fonts) and click on a font to see its font file name. - On Mac, you can find font file names using
Font Book(not tested)
Are values expected to be in specific units?
No
Special Notes
None
SO_indiScale
What does it do?
deprecated since v0.4, use SO_individualScale instead.
Default value:
What values can it take?
deprecated since v0.4, use SO_individualScale instead.
Are values expected to be in specific units?
No
Special Notes
None
SO_indiScale3factor
What does it do?
Defines the central area to use when SO_individualScale=3. If it is set to 0.2, the central area is the part of the frame that remains after excluding 20% of frame width on left and right; and 20% of frame height on the top and bottom.
Default value: 0.2
What values can it take?
A number between 0 and 0.5
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_individualScale
SO_individualScale
What does it do?
Specifies the method for choosing the upper and lower limit of values of the overview frame. In other words, specifies the data values that are to correspond to the bottom-most and top-most color of the colormap.
Default value: 0
What values can it take?
An integer value in either x or yx format (0-6, 10-16, 20-26). Valid values for x are:
- 0 or 1: lower end is set to the value of the flag "SO_MV_scalemin" and the upper end to the value of the flag "SO_MV_scalemax"
- 2: lower end is set to the minimum value of the entire movie, where "minimum" is interpreted based on the the flag SO_percentileScale. Similarly, the upper end is set to the maximum value of the entire movie.
- 3: Similar to when 2, but the minimum and maximum values are calculated using a central region of the movie defined by the flag SO_indiScale3factor
- 4: lower end is set to the flag SO_MV_scalemin, upper end is set as when 2.
- 5: lower end is set to the minimum of the region defined by the mask contained in the associated ".Area" or ".area.tif" file in the folder "Coor". Similarly the upper end is set to the maximum of the region.
- 6: lower end is set to the value of the flag SO_MV_scalemin, the upper end is set as in when 5.
Valid values for y are:
1:scale minimum to 0 and 0 to maximum separatedly into lower and upper half range
2:center scaling at 0, adapt minimum or maximum accordingly
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_indiScale3factor, SO_percentageScale, SO_percentageValue
SO_lowerThreshPositiveResps
What does it do?
Indicates a lower threshold, which is applied to the data indicated in SO_thresholdOn. Pixels with values higher than this threshold will be colorized. Ignored if SO_thresholdOn is 'none'
Default value: a0
What values can it take?
A string value. Absolute and relative thresholds can be specified for this flag.
- For absolute thresholds use the format 'axxxx'. E.g.: 'a956.56', in which case all pixels with value higher than 956.56 will be colorized.
- For relative threholds use the format 'ryyyy'. E.g.: 'r34.56', in which case all pixels with values in the range 34.56%-100% of the data range will be colorized.
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_thresholdOn, SO_upperThreshNegativeResps
SO_Method
What does it do?
Indicates whether CTVs are calculated pixel-wise or frame-wise.
Default value: 10
What values can it take?
Integer values. Valid ones are:
- 0 for calculations pixel by pixel (i.e. on the time-course in each pixel).
- 10 for calculations frame by frame (much faster, but not all functions are possible).
Are values expected to be in specific units?
No
Special Notes
Related flags: CTV_Method
SO_percentileScale
What does it do?
Indicates if percentile values specified in SO_percentileValue should be used instead on minimum and maximum while scaling data for generating overviews
Default value: False
What values can it take?
A boolean value (True/False)
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_percentileValue
SO_percentileValue
What does it do?
Indicates a percentile value. Only used if SO_percentileScale is True. Data will be scaled to map the value at 'SO_percentileScale'th percentile to the bottom-most color and '100-SO_percentileScale'th percentile to the top-most color.
Default value: 0
What values can it take?
Number between 0 and 100
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_percentileScale
SO_reverseIt
What does it do?
Specifies whether to flip horizontally (i.e. left-right) the overview frame. Is identical to SO_rotateImage eq 7. 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
SO_rotateImage
What does it do?
Specifies the rotation to be applied to the overview frame. When set to 0, no rotation is applied. This flag emulates the IDL command 'rotate'.
Default value: 0
What values can it take?
An integer value.
- 0: no rotation,
- 1: 90cw
- 2: 180cw
- 3: 270cw
- 4: flip horizontally (left-right) and 90cw
- 5: flip horizontally (left-right)
- 6: flip vertically (up-down) and 90cw
- 7: flip vertically (up-down)
Are values expected to be in specific units?
No
Special Notes
None
SO_scaleLegendFactor
What does it do?
Specifies the factor by which the upper and lower limits of the data are multiplied before being printed above and below the colorbar
Default value: 1
What values can it take?
A number
Are values expected to be in specific units?
No
Special Notes
Related flags: CTV_scalebar
SO_showROIs
What does it do?
Overlay other information to overview output.
Default value: 0
What values can it take?
0 or integers greater than 10. Currently, the tenths (second-last) digit indicates:
- 0: do nothing
- 1: puts unfilled squares/circles/polygons with the foreground color specified in the flag 'SO_fgColor'
- 2: same as 1, but the squares/circles/polygons have different colors and the overview frame underneath is replaced by all background.
AND
the units (last) digit indicates the source from which ROI information is sourced. See the documentation of the flag RM_ROITrace for this.
E.g.: SO_showROIs=14. The tenths digit is 1, so it puts unfilled ROIs and units digit is 4, so the info will be sourced from the .roi.tif file
Are values expected to be in specific units?
No
Special Notes
SO_thresholdOn
What does it do?
Indicates the variable that is thresholded to decide the region of the overview frame that is colorized.
Default value: none
What values can it take?
A string value. Valid values are
- none: all pixels will be colorized, subject to the flag SO_withinArea. This is the default setting.
- foto1: foto data calculated from raw data will be used
- overview: overview data calculated from sig1 will be used
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_lowerThreshPositiveResps, SO_upperThreshNegativeResps
SO_thresholdOnValue
What does it do?
deprecated since v0.4.1, please use the flags SO_upperThreshNegativeResps and SO_lowerThreshPositiveResps instead
Default value:
What values can it take?
deprecated since v0.4.1, please use the flags SO_upperThreshNegativeResps and SO_lowerThreshPositiveResps instead
Are values expected to be in specific units?
No
Special Notes
None
SO_thresholdScale
What does it do?
Indicates how data outside the region of focus is to be scaled and mapped to gray values. Ignored if SO_thresholdShowImage is 'bgColor'.
Default value: full
What values can it take?
A string value. For example, when SO_thresholdShowImage is 'foto1', black and white are respectively mapped onto the minimum and maximum of foto data restricted to:
- full: no restriction. all foto data is used to calculate minimum and maximum
- onlyShown: restricted to the region outside the region of focus
Are values expected to be in specific units?
No
Special Notes
Related flag: SO_thresholdShowImage
SO_thresholdShowImage
What does it do?
Indicates the data to be shown outside the region of focus defined by SO_thresholdOn, SO_lowerThreshPositiveResps, SO_upperThreshNegativeResps and SO_withinArea.
Default value: foto1
What values can it take?
A string value. Valid values are:
- foto1: foto data calculated from raw data will be used. This is the default setting. Since foto data is a frame, the region outside the region of focus will be the same for all frames
- bgColor: no data is shown. All pixels outside the region of focus are set to the SO_bgColor
Are values expected to be in specific units?
No
Special Notes
Related flag: SO_thresholdScale
SO_upperThreshNegativeResps
What does it do?
Indicates an upper threshold, which is applied to the data indicated in SO_thresholdOn. Pixels with values lower than this threshold will be colorized. Ignored if 'mv_thresholdOn' is 'none'
Default value: a0
What values can it take?
A string value. Absolute and relative thresholds can be specified for this flag.
- For absolute thresholds use the format 'axxxx'. E.g.: 'a956.56', in which case all pixels with value lower than 956.56 will be colorized.
- For relative threholds use the format 'ryyyy'. E.g.: 'r34.56', in which case all pixels with values in the range 0%-34.56% of the data range will be colorized.
Are values expected to be in specific units?
No
Special Notes
Related flags: SO_thresholdOn, SO_lowerThreshPositiveResps
SO_withinArea
What does it do?
indicates whether SO_MV_colortable-based data colorization in overviews is restricted to an area indicated by the .area/.area.tif file for this measurement/animal
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
SO_withMask
What does it do?
deprecated since v0.4, use SO_withinArea instead
Default value:
What values can it take?
deprecated since v0.4, use SO_withinArea instead
Are values expected to be in specific units?
No
Special Notes
None
SO_xgap
What does it do?
Specifies the width of the padding added to the right of the overview frame, which is double this value in pixels. Only used when CTV_scalebar is True.
Default value: 0
What values can it take?
Integers
Are values expected to be in specific units?
Yes, pixels (double this value = width of padding pixels)
Special Notes
Related flag: CTV_scalebar