-
Notifications
You must be signed in to change notification settings - Fork 9
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added ROI info interface which displays statistics about each ROI for…
… a given ion image (as well as a second interface for viewing stats for all ion images). Can copy figures to clipboard and export data to CSV.
- Loading branch information
Showing
6 changed files
with
287 additions
and
5 deletions.
There are no files selected for viewing
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| classdef RegionOfInterestAllInfoFigure < Figure | ||
|
|
||
| properties (Access = private) | ||
| roiList; | ||
| imageList; | ||
|
|
||
| regionOfInterestTable; | ||
| exportButton; | ||
| previousPath; | ||
| end | ||
|
|
||
| methods | ||
| function this = RegionOfInterestAllInfoFigure(roiList, imageList) | ||
| this.roiList = roiList; | ||
| this.imageList = imageList; | ||
|
|
||
| this.setTitle('All Region of Interest Details'); | ||
|
|
||
| this.updateData(); | ||
| end | ||
|
|
||
| function updateData(this) | ||
| index = 1; | ||
|
|
||
| tableData = {}; | ||
|
|
||
| for j = 1:length(this.imageList) | ||
| image = this.imageList(j); | ||
|
|
||
| for i = 1:this.roiList.getSize() | ||
| roi = this.roiList.get(i); | ||
|
|
||
| tableData{index, 1} = image.description; | ||
| tableData{index, 2} = ['<HTML><font color="' roi.getColour().toHex() '">' roi.getName() '</font></HTML>' ];%roi.name; | ||
| tableData{index, 3} = mean(image.imageData(roi.pixelSelection)); | ||
| tableData{index, 4} = std(image.imageData(roi.pixelSelection)); | ||
| tableData{index, 5} = sum(roi.pixelSelection(:)); | ||
| tableData{index, 6} = max(image.imageData(roi.pixelSelection)); | ||
| tableData{index, 7} = min(image.imageData(roi.pixelSelection)); | ||
|
|
||
| index = index + 1; | ||
| end | ||
| end | ||
|
|
||
| set(this.regionOfInterestTable, 'Data', tableData); | ||
| end | ||
|
|
||
| function export(this) | ||
| [filename, path, filter] = uiputfile({'*.csv', 'CSV File'}, 'Export to CSV', [this.previousPath filesep 'ROIDetails.csv']); | ||
|
|
||
| if(filter > 0) | ||
| this.previousPath = path; | ||
| location = [path filesep filename]; | ||
|
|
||
| [fid, errmsg] = fopen(location, 'w'); | ||
|
|
||
| if(fid < 0) | ||
| errordlg(errmsg, 'Could not export to CSV'); | ||
| else | ||
| fprintf(fid, 'm/z, ROI, Mean, SD, #Pixels, Max, Min\n'); | ||
|
|
||
| for j = 1:length(this.imageList) | ||
| selectedImage = this.imageList(j); | ||
|
|
||
| for i = 1:this.roiList.getSize() | ||
| roi = this.roiList.get(i); | ||
|
|
||
| fprintf(fid, '%s,%s,%f,%f,%d,%f,%f\n', selectedImage.description, roi.getName(), ... | ||
| mean(selectedImage.imageData(roi.pixelSelection)), ... | ||
| std(selectedImage.imageData(roi.pixelSelection)), ... | ||
| sum(roi.pixelSelection(:)), ... | ||
| max(selectedImage.imageData(roi.pixelSelection)), ... | ||
| min(selectedImage.imageData(roi.pixelSelection))); | ||
| end | ||
| end | ||
|
|
||
| fclose(fid); | ||
| end | ||
| end | ||
| end | ||
| end | ||
|
|
||
| methods (Access = protected) | ||
| function createFigure(this) | ||
| % createFigure Create figure. | ||
| % | ||
| % createFigure() | ||
|
|
||
| createFigure@Figure(this); | ||
|
|
||
| columnNames = {'m/z', 'ROI', 'Mean', 'SD', '# Pixels', 'Max', 'Min'}; | ||
| columnFormat = {'numeric', 'char', 'numeric', 'numeric', 'numeric', 'numeric', 'numeric'}; | ||
| columnEditable = [false, false, false, false, false, false, false]; | ||
|
|
||
| this.regionOfInterestTable = uitable('Parent', this.handle, ... | ||
| 'ColumnName', columnNames, 'ColumnFormat', columnFormat, 'ColumnEditable', columnEditable, ... | ||
| 'RowName', [], 'Units', 'normalized', 'Position', [0.05 0.15 0.9 0.8]); | ||
| this.exportButton = uicontrol('Parent', this.handle, ... | ||
| 'String', 'Export', 'Units', 'normalized', 'Position', [0.75, 0.05, 0.2, 0.05], 'Callback', @(src, event) this.export()); | ||
| end | ||
| end | ||
| end |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| classdef RegionOfInterestInfoFigure < Figure | ||
|
|
||
| properties (Access = private) | ||
| roiList; | ||
| imageList; | ||
|
|
||
| imageListSelection; | ||
| allDataButton; | ||
| imageDisplay; | ||
| roiPlot; | ||
| regionOfInterestTable; | ||
|
|
||
| previousPath; | ||
|
|
||
| copyToClipboardButton; | ||
| exportButton; | ||
| end | ||
|
|
||
| methods | ||
| function this = RegionOfInterestInfoFigure(roiList, imageList) | ||
| this.roiList = roiList; | ||
| this.imageList = imageList; | ||
|
|
||
| this.setTitle('Region of Interest Details'); | ||
| this.updateList(); | ||
| end | ||
|
|
||
| function updateList(this) | ||
| set(this.imageListSelection, 'String', {this.imageList.description}); | ||
|
|
||
| this.imageDisplay.removeAllRegionsOfInterest(); | ||
|
|
||
| for i = 1:this.roiList.getSize() | ||
| roi = this.roiList.get(i); | ||
|
|
||
| this.imageDisplay.addRegionOfInterest(roi); | ||
| end | ||
| end | ||
|
|
||
| function selectImageIndex(this, index) | ||
| set(this.imageListSelection, 'Value', index); | ||
| this.imageSelected([], []); | ||
| end | ||
|
|
||
| function viewAllData(this) | ||
| RegionOfInterestAllInfoFigure(this.roiList, this.imageList); | ||
| end | ||
|
|
||
| function copyToClipboard(this) | ||
| this.setVisibilityForControls('off'); | ||
| print -clipboard -dmeta | ||
| this.setVisibilityForControls('on'); | ||
| end | ||
|
|
||
| function export(this) | ||
| selectedValue = get(this.imageListSelection, 'Value'); | ||
| selectedImage = this.imageList(selectedValue); | ||
|
|
||
| [filename, path, filter] = uiputfile({'*.csv', 'CSV File'}, 'Export to CSV', [this.previousPath filesep selectedImage.description '.csv']); | ||
|
|
||
| if(filter > 0) | ||
| this.previousPath = path; | ||
| location = [path filesep filename]; | ||
|
|
||
| [fid, errmsg] = fopen(location, 'w'); | ||
|
|
||
| if(fid < 0) | ||
| errordlg(errmsg, 'Could not export to CSV'); | ||
| else | ||
| fprintf(fid, 'ROI, Mean, SD, #Pixels, Max, Min\n'); | ||
|
|
||
| for i = 1:this.roiList.getSize() | ||
| roi = this.roiList.get(i); | ||
|
|
||
| fprintf(fid, '%s,%f,%f,%d,%f,%f\n', roi.getName(), ... | ||
| mean(selectedImage.imageData(roi.pixelSelection)), ... | ||
| std(selectedImage.imageData(roi.pixelSelection)), ... | ||
| sum(roi.pixelSelection(:)), ... | ||
| max(selectedImage.imageData(roi.pixelSelection)), ... | ||
| min(selectedImage.imageData(roi.pixelSelection))); | ||
| end | ||
|
|
||
| fclose(fid); | ||
| end | ||
| end | ||
| end | ||
| end | ||
|
|
||
| methods (Access = protected) | ||
| function setVisibilityForControls(this, visibility) | ||
| set(this.imageListSelection, 'Visible', visibility); | ||
| set(this.allDataButton, 'Visible', visibility); | ||
| set(this.copyToClipboardButton, 'Visible', visibility); | ||
| set(this.exportButton, 'Visible', visibility); | ||
| end | ||
|
|
||
| function imageSelected(this, source, event) | ||
| selectedImageIndex = get(this.imageListSelection, 'Value'); | ||
| selectedImage = this.imageList(selectedImageIndex); | ||
|
|
||
| this.imageDisplay.setData(selectedImage); | ||
|
|
||
| tableData = {}; | ||
|
|
||
| colourTable = []; | ||
|
|
||
| axes(this.roiPlot); | ||
|
|
||
| for i = 1:this.roiList.getSize() | ||
| roi = this.roiList.get(i); | ||
|
|
||
| colour = [roi.getColour().r roi.getColour().g roi.getColour().b]; | ||
|
|
||
| if(i == 2) | ||
| hold on; | ||
| end | ||
| bar(i, mean(selectedImage.imageData(roi.pixelSelection)), 'FaceColor', colour ./ 255); | ||
|
|
||
| tableData{i, 1} = ['<HTML><font color="' roi.getColour().toHex() '">' roi.getName() '</font></HTML>' ];%roi.name; | ||
| tableData{i, 2} = mean(selectedImage.imageData(roi.pixelSelection)); | ||
| tableData{i, 3} = std(selectedImage.imageData(roi.pixelSelection)); | ||
| tableData{i, 4} = sum(roi.pixelSelection(:)); | ||
| tableData{i, 5} = max(selectedImage.imageData(roi.pixelSelection)); | ||
| tableData{i, 6} = min(selectedImage.imageData(roi.pixelSelection)); | ||
| end | ||
| assignin('base', 'tableData', tableData); | ||
| set(this.regionOfInterestTable, 'Data', tableData); | ||
|
|
||
| errorbar(1:this.roiList.getSize(), [tableData{:, 2}], [tableData{:, 3}], '.'); | ||
| set(gca, 'XTickLabel', '') | ||
|
|
||
| hold off; | ||
| end | ||
|
|
||
| function createFigure(this) | ||
| % createFigure Create figure. | ||
| % | ||
| % createFigure() | ||
|
|
||
| createFigure@Figure(this); | ||
|
|
||
| columnNames = {'ROI', 'Mean', 'SD', '# Pixels', 'Max', 'Min'}; | ||
| columnFormat = {'char', 'numeric', 'numeric', 'numeric', 'numeric', 'numeric'}; | ||
| columnEditable = [false, false, false, false, false, false]; | ||
|
|
||
| this.imageListSelection = uicontrol('Parent', this.handle, 'Style', 'popup', ... | ||
| 'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.7, 0.1], 'Callback', @(src, event) this.imageSelected(src, event)); | ||
|
|
||
| this.allDataButton = uicontrol('Parent', this.handle, ... | ||
| 'String', 'View all data', 'Units', 'normalized', 'Position', [0.75, 0.9, 0.2, 0.05], 'Callback', @(src, event) this.viewAllData()); | ||
|
|
||
| this.imageDisplay = ImageDisplay(this, Image(1)); | ||
| set(this.imageDisplay.axisHandle, 'Position', [0.05, 0.5, 0.4, 0.35]); | ||
|
|
||
| this.roiPlot = axes(this.handle, 'Units', 'normalized', 'Position', [0.525, 0.525, 0.425, 0.325]); | ||
|
|
||
| this.regionOfInterestTable = uitable('Parent', this.handle, ... | ||
| 'ColumnName', columnNames, 'ColumnFormat', columnFormat, 'ColumnEditable', columnEditable, ... | ||
| 'RowName', [], 'Units', 'normalized', 'Position', [0.05 0.15 0.9 0.3]); | ||
|
|
||
| this.copyToClipboardButton = uicontrol('Parent', this.handle, ... | ||
| 'String', 'Copy to clipboard', 'Units', 'normalized', 'Position', [0.05, 0.05, 0.2, 0.05], 'Callback', @(src, event) this.copyToClipboard()); | ||
| this.exportButton = uicontrol('Parent', this.handle, ... | ||
| 'String', 'Export', 'Units', 'normalized', 'Position', [0.75, 0.05, 0.2, 0.05], 'Callback', @(src, event) this.export()); | ||
| end | ||
| end | ||
| end |