diff --git a/README.md b/README.md index 2f9de2f..0d967b7 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,12 @@ A Graphical User Interface for MSI in Julia: https://github.com/CINVESTAV-LABI/j unzip the file in your desired location
## Load User Interface -1. Set working directory to Julia_msi_GUI (this repository) in your terminal using: - linux: +1. Set working directory to Julia_msi_GUI (this repository) in your terminal using:
+ Linux: ``` cd PathToRepository/Julia_msi_GUI-main ``` - windows/mac: + Windows/Mac: ``` cd PathToRepository\Julia_msi_GUI-main ``` @@ -24,7 +24,7 @@ A Graphical User Interface for MSI in Julia: https://github.com/CINVESTAV-LABI/j ``` 3. After the script has finished loading, it should open a page (http://127.0.0.1:1481/) in your browser with the web app running. -Additional notes: -After the first boot initializes the packages in your computer, subsequent uses of the app should not take longer to load. -Recomended system requirements: 4 core processor, 8 GB ram -Minimum system requirements: 2 core processor, 8 GB ram (long loading times) \ No newline at end of file +Additional notes:
+After the first boot initializes the packages in your computer, subsequent uses of the app should not take longer to load.
+Recomended system requirements: 4 core processor, 8 GB ram
+Minimum system requirements: 2 core processor, 8 GB ram (long loading times)
\ No newline at end of file diff --git a/app.jl b/app.jl index f1a52a6..9eef788 100644 --- a/app.jl +++ b/app.jl @@ -15,18 +15,18 @@ using NativeFileDialog # Opens the file explorer depending on the OS using StipplePlotly @genietools -# ==Code import == +# == Code import == # add your data analysis code here or in the lib folder. Code in lib/ will be # automatically loaded rgb_ViridisPalette=reinterpret(ColorTypes.RGB24, ViridisPalette) -# ==Search functions == +# == Search functions == function increment_image(current_image, image_list) if isempty(image_list) return nothing end current_index=findfirst(isequal(current_image), image_list) - if current_index ==nothing || current_index ==length(image_list) || current_image ==="" + if current_index==nothing || current_index==length(image_list) || current_image ==="" return image_list[length(image_list)] # Return the current image if it's the last one or not found else return image_list[current_index + 1] # Move to the next image @@ -38,17 +38,215 @@ function decrement_image(current_image, image_list) return nothing end current_index=findfirst(isequal(current_image), image_list) - if current_index ==nothing || current_index ==1 || current_image ==="" + if current_index==nothing || current_index==1 || current_image==="" return image_list[1] # Return the current image if it's the first one or not found else return image_list[current_index - 1] # Move to the previous image end end -# ==Reactive code == +## Plot Image functions +# loadImgPlot recieves the local directory of the image as a string, +# returns the layout and data for the heatmap plotly plot +# this function loads the image into a plot +function loadImgPlot(interfaceImg::String) + # Load the image + cleaned_img=replace(interfaceImg, r"\?.*" => "") + cleaned_img=lstrip(cleaned_img, '/') + var=joinpath("./public", cleaned_img) + img=load(var) + # Convert to grayscale + img_gray=Gray.(img) + img_array=Array(img_gray) + #println(typeof(img_array)) + elevation=Float32.(Array(img_gray)) + #println(typeof(elevation)) + # Get the X, Y coordinates of the image + height, width = size(img_array) + #println("height: $(height), width: $(width)") + X = collect(1:width) + Y = collect(1:height) + + # Create the layout + layout = PlotlyBase.Layout( + xaxis = PlotlyBase.attr( + visible = false, + scaleanchor = "y" + ), + yaxis = PlotlyBase.attr( + visible = false + ) + ) + + # Create the trace for the image + trace = PlotlyBase.heatmap( + z = elevation, + x = X, + y = -Y, + name="", + showlegend=false, + colorscale = "Viridis", + showscale = true, + colorbar = attr( + title = attr( + text = "Intensity", + font = attr( + size = 14, + color = "black" + ), + side = "right" + ), + ticks = "outside", + ticklen = 2, + tickwidth = 0.5, + nticks = 5, + tickformat = ".2g" + ) + ) + + plotdata = [trace] + plotlayout = layout + return plotdata, plotlayout, width, height +end +# loadContourPlot recieves the local directory of the image as a string, +# returns the layout and data for the contour plotly plot +# this function loads the image and applies a gaussian filter +# to smoothen it and loads it into a plot +function loadContourPlot(interfaceImg::String) + # Load the image + cleaned_img=replace(interfaceImg, r"\?.*" => "") + cleaned_img=lstrip(cleaned_img, '/') + var=joinpath("./public", cleaned_img) + img=load(var) + img_gray=Gray.(img) + img_array=Array(img_gray) + elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 + + # Smooth the image + sigma=3.0 + kernel=Kernel.gaussian(sigma) + elevation_smoothed=imfilter(elevation, kernel) + + # Create the X, Y meshgrid coordinates + x=1:size(elevation_smoothed, 2) + y=1:size(elevation_smoothed, 1) + X=repeat(reshape(x, 1, length(x)), length(y), 1) + Y=repeat(reshape(y, length(y), 1), 1, length(x)) + + layout=PlotlyBase.Layout( + title="2D Topographic Map", + xaxis=PlotlyBase.attr( + title="X", + scaleanchor="y" + ), + yaxis=PlotlyBase.attr( + title="Y" + ), + ) + trace=PlotlyBase.contour( + z=elevation_smoothed, + x=X[1, :], # Use the first row + y=-Y[:, 1], # Use the first column + contours_coloring="Viridis", + colorscale="Viridis", + colorbar = attr( + tickformat = ".2g" + ) + ) + plotdata = [trace] + plotlayout = layout + return plotdata, plotlayout +end +# loadSurfacePlot recieves the local directory of the image as a string, +# returns the layout and data for the surface plotly plot +# this function loads the image and applies a gaussian filter +# to smoothen it and loads it into a 3D plot +function loadSurfacePlot(interfaceImg::String) + # Load the image + cleaned_img=replace(interfaceImg, r"\?.*" => "") + cleaned_img=lstrip(cleaned_img, '/') + var=joinpath("./public", cleaned_img) + img=load(var) + #println("Image type:", typeof(img)) + img_gray=Gray.(img) # Convert to grayscale + #println("Grayscale image type:", typeof(img_gray)) + img_array=Array(img_gray) + elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 + #println("Elevation size:", size(elevation)) + # Smooth the image + sigma=3.0 + kernel=Kernel.gaussian(sigma) + #println(size(kernel)) + elevation_smoothed=imfilter(elevation, kernel) + #println("Smoothed elevation size:", size(elevation_smoothed)) + # Transpose the elevation_smoothed array + # Create the X, Y meshgrid coordinates + x=1:size(elevation_smoothed, 2) + y=1:size(elevation_smoothed, 1) + X=repeat(reshape(x, 1, length(x)), length(y), 1) + #println("Size of X:", size(X)) + Y=repeat(reshape(y, length(y), 1), 1, length(x)) + #println("Size of Y:", size(Y)) + # Calculate the number of ticks and aspect ratio for the 3d plot + x_nticks=min(20, length(x)) + y_nticks=min(20, length(y)) + z_nticks=5 + aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5) + # Define the layout for the 3D plot + layout3D=PlotlyBase.Layout( + title="3D Surface Plot", + scene=attr( + xaxis_nticks=x_nticks, + yaxis_nticks=y_nticks, + zaxis_nticks=z_nticks, + camera=attr(eye=attr(x=0, y=-1, z=0.5)), + aspectratio=aspect_ratio + ) + ) + if size(elevation_smoothed, 1) < size(elevation_smoothed, 2) + # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping + elevation_smoothed=transpose(elevation_smoothed) + Y=-Y + end + + trace3D=PlotlyBase.surface( + x=X[1, :], + y=Y[:, 1], + z=elevation_smoothed, + contours_z=attr( + show=true, + usecolormap=true, + highlightcolor="limegreen", + project_z=true + ), + colorscale="Viridis", + colorbar = attr( + tickformat = ".2g" + ) + ) + plotdata = [trace3D] + plotlayout = layout3D + return plotdata, plotlayout +end + +function crossLinesPlot(x, y, maxwidth, maxheight) + # Define the coordinates for the two lines + l1_x = [0, maxwidth] + l1_y = [y, y] + l2_x = [x, x] + l2_y = [0, maxheight] + + # Create the line traces + trace1 = PlotlyBase.scatter(x = l1_x, y = l1_y, mode = "lines",line=attr(color="red", width=0.5),name="Line X",showlegend=false) + trace2 = PlotlyBase.scatter(x = l2_x, y = l2_y, mode = "lines",line=attr(color="red", width=0.5),name="Line Y",showlegend=false) + + return trace1, trace2 +end + +# == Reactive code == # reactive code to make the UI interactive @app begin - # ==Reactive variables == + # == Reactive variables == # reactive variables exist in both the Julia backend and the browser with two-way synchronization # @out variables can only be modified by the backend # @in variables can be modified by both the backend and the browser @@ -107,8 +305,8 @@ end @out imgIntT="/.bmp" # image Interface TrIQ @out colorbar="/.png" @out colorbarT="/.png" - @out img_width=0 - @out img_height=0 + @out imgWidth=0 + @out imgHeight=0 # Messages to interface variables @out msg="" @@ -141,6 +339,22 @@ end @out eTime=time() ## Plots + # Local image to plot + layoutImg = PlotlyBase.Layout( + xaxis = PlotlyBase.attr( + visible = false, + scaleanchor = "y" + ), + yaxis = PlotlyBase.attr( + visible = false + ) + ) + traceImg=PlotlyBase.heatmap(x=[], y=[]) + @out plotdataImg = [traceImg] + @out plotlayoutImg = layoutImg + # For triq image + @out plotdataImgT = [traceImg] + @out plotlayoutImgT = layoutImg # Interface Plot Spectrum layoutSpectra=PlotlyBase.Layout( title="SUM Spectrum plot", @@ -216,7 +430,7 @@ end @out plotdata3d=[trace3D] @out plotlayout3d=layout3D - # ==Reactive handlers == + # == Reactive handlers == # Reactive handlers watch a variable and execute a block of code when its value changes # The onbutton handler will set the variable to false after the block is executed @@ -238,6 +452,8 @@ end btnSpectraDisable=false SpectraEnabled=true end + xCoord=0 + yCoord=0 end end @@ -271,11 +487,12 @@ end img=reverse(permutedims(img, (2, 1)), dims=1) end flipped_img=reverse(img, dims=1) - img_width=size(flipped_img, 2) - img_height=size(flipped_img, 1) + imgWidth=size(flipped_img, 2) + imgHeight=size(flipped_img, 1) save(image_path, flipped_img) # Use timestamp to refresh image interface container imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)" + plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) # Get current image current_triq="TrIQ_$(text_nmass).bmp" msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" @@ -305,11 +522,12 @@ end img=reverse(permutedims(img, (2, 1)), dims=1) end flipped_img=reverse(img, dims=1) - img_width=size(flipped_img, 2) - img_height=size(flipped_img, 1) + imgWidth=size(flipped_img, 2) + imgHeight=size(flipped_img, 1) save(image_path, flipped_img) # Use timestamp to refresh image interface container imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)" + plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) # Get current image current_msi="MSI_$(text_nmass).bmp" msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" @@ -466,15 +684,22 @@ end new_msi=decrement_image(current_msi, msi_bmp) new_col_msi=decrement_image(current_col_msi, col_msi_png) - - current_msi=new_msi - current_col_msi=new_col_msi - imgInt="/$(current_msi)?t=$(timestamp)" - colorbar="/$(current_col_msi)?t=$(timestamp)" + if new_msi!=nothing || new_col_msi!=nothing + current_msi=new_msi + current_col_msi=new_col_msi + imgInt="/$(current_msi)?t=$(timestamp)" + colorbar="/$(current_col_msi)?t=$(timestamp)" - text_nmass=replace(current_msi, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" + text_nmass=replace(current_msi, "MSI_" => "") + text_nmass=replace(text_nmass, ".bmp" => "") + msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" + # Process the image in the function + plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) + else + traceImg=PlotlyBase.heatmap(x=[], y=[]) + plotdataImg = [traceImg] + msgimg = "" + end end @onbutton imgPlus begin # Append a query string to force the image to refresh @@ -485,53 +710,75 @@ end new_msi=increment_image(current_msi, msi_bmp) new_col_msi=increment_image(current_col_msi, col_msi_png) + if new_msi!=nothing || new_col_msi!=nothing + current_msi=new_msi + current_col_msi=new_col_msi + imgInt="/$(current_msi)?t=$(timestamp)" + colorbar="/$(current_col_msi)?t=$(timestamp)" - current_msi=new_msi - current_col_msi=new_col_msi - imgInt="/$(current_msi)?t=$(timestamp)" - colorbar="/$(current_col_msi)?t=$(timestamp)" - - text_nmass=replace(current_msi, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" + text_nmass=replace(current_msi, "MSI_" => "") + text_nmass=replace(text_nmass, ".bmp" => "") + msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" + # Process the image in the function + plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) + else + traceImg=PlotlyBase.heatmap(x=[], y=[]) + plotdataImg = [traceImg] + msgimg = "" + end end @onbutton imgMinusT begin # Append a query string to force the image to refresh timestamp=string(time_ns()) - new_msi=decrement_image(current_triq, triq_bmp) - new_col_msi=decrement_image(current_col_triq, col_triq_png) # Update the array of images with TrIQ filter listed in the public folder triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) - current_triq=new_msi - current_col_triq=new_col_msi - imgIntT="/$(current_triq)?t=$(timestamp)" - colorbarT="/$(current_col_triq)?t=$(timestamp)" + new_msi=decrement_image(current_triq, triq_bmp) + new_col_msi=decrement_image(current_col_triq, col_triq_png) + if new_msi!=nothing || new_col_msi!=nothing + current_triq=new_msi + current_col_triq=new_col_msi + imgIntT="/$(current_triq)?t=$(timestamp)" + colorbarT="/$(current_col_triq)?t=$(timestamp)" - text_nmass=replace(current_triq, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" - + text_nmass=replace(current_triq, "TrIQ_" => "") + text_nmass=replace(text_nmass, ".bmp" => "") + msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" + # Process the image in the function + plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) + else + traceImg=PlotlyBase.heatmap(x=[], y=[]) + plotdataImgT = [traceImg] + msgtriq = "" + end end @onbutton imgPlusT begin # Append a query string to force the image to refresh timestamp=string(time_ns()) - new_msi=increment_image(current_triq, triq_bmp) - new_col_msi=increment_image(current_col_triq, col_triq_png) # Update the array of images with TrIQ filter listed in the public folder triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) - - current_triq=new_msi - current_col_triq=new_col_msi - imgIntT="/$(current_triq)?t=$(timestamp)" - colorbarT="/$(current_col_triq)?t=$(timestamp)" - text_nmass=replace(current_triq, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" + new_msi=increment_image(current_triq, triq_bmp) + new_col_msi=increment_image(current_col_triq, col_triq_png) + if new_msi!=nothing || new_col_msi!=nothing + current_triq=new_msi + current_col_triq=new_col_msi + imgIntT="/$(current_triq)?t=$(timestamp)" + colorbarT="/$(current_col_triq)?t=$(timestamp)" + + text_nmass=replace(current_triq, "TrIQ_" => "") + text_nmass=replace(text_nmass, ".bmp" => "") + msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" + # Process the image in the function + plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) + else + traceImg=PlotlyBase.heatmap(x=[], y=[]) + plotdataImgT = [traceImg] + msgtriq = "" + end end # 3d plot @@ -548,59 +795,7 @@ end btnStartDisable=true btnSpectraDisable=true try - img=load(var) - #println("Image type:", typeof(img)) - img_gray=Gray.(img) # Convert to grayscale - #println("Grayscale image type:", typeof(img_gray)) - img_array=Array(img_gray) - elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 - #println("Elevation size:", size(elevation)) - # Smooth the image - sigma=3.0 - kernel=Kernel.gaussian(sigma) - #println(size(kernel)) - elevation_smoothed=imfilter(elevation, kernel) - #println("Smoothed elevation size:", size(elevation_smoothed)) - # Transpose the elevation_smoothed array - # Create the X, Y meshgrid coordinates - x=1:size(elevation_smoothed, 2) - y=1:size(elevation_smoothed, 1) - X=repeat(reshape(x, 1, length(x)), length(y), 1) - #println("Size of X:", size(X)) - Y=repeat(reshape(y, length(y), 1), 1, length(x)) - #println("Size of Y:", size(Y)) - # Calculate the number of ticks and aspect ratio for the 3d plot - x_nticks=min(20, length(x)) - y_nticks=min(20, length(y)) - z_nticks=5 - aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5) - - # Define the layout for the 3D plot - layout3D=PlotlyBase.Layout( - title="3D Surface Plot", - scene=attr( - xaxis_nticks=x_nticks, - yaxis_nticks=y_nticks, - zaxis_nticks=z_nticks, - camera=attr(eye=attr(x=0, y=-1, z=0.5)), - aspectratio=aspect_ratio - ) - ) - if size(elevation_smoothed, 1) < size(elevation_smoothed, 2) - # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping - elevation_smoothed=transpose(elevation_smoothed) - Y=-Y - end - - trace3D=PlotlyBase.surface(x=X[1, :], y=Y[:, 1], z=elevation_smoothed, - contours_z=attr( - show=true, - usecolormap=true, - highlightcolor="limegreen", - project_z=true - ), colorscale="Viridis") - plotdata3d=[trace3D] # We add the data from the image to the plot - plotlayout3d=layout3D # we update the style of the plot to fit the image. + plotdata3d, plotlayout3d = loadSurfacePlot(imgInt) GC.gc() # Trigger garbage collection if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS @@ -641,53 +836,7 @@ end btnStartDisable=true btnSpectraDisable=true try - img=load(var) - img_gray=Gray.(img) # Convert to grayscale - img_array=Array(img_gray) - elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 - # Smooth the image - sigma=3.0 - kernel=Kernel.gaussian(sigma) - elevation_smoothed=imfilter(elevation, kernel) - - # Create the X, Y meshgrid coordinates - x=1:size(elevation_smoothed, 2) - y=1:size(elevation_smoothed, 1) - X=repeat(reshape(x, 1, length(x)), length(y), 1) - Y=repeat(reshape(y, length(y), 1), 1, length(x)) - - # Calculate the number of ticks and aspect ratio for the 3d plot - x_nticks=min(20, length(x)) - y_nticks=min(20, length(y)) - z_nticks=5 - aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5) - - # Define the layout for the 3D plot - layout3D=PlotlyBase.Layout( - title="3D Surface Plot", - scene=attr( - xaxis_nticks=x_nticks, - yaxis_nticks=y_nticks, - zaxis_nticks=z_nticks, - camera=attr(eye=attr(x=0, y=-1, z=0.5)), - aspectratio=aspect_ratio - ) - ) - if size(elevation_smoothed, 1) < size(elevation_smoothed, 2) - # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping - elevation_smoothed=transpose(elevation_smoothed) - Y=-Y - end - - trace3D=PlotlyBase.surface(x=X[1, :], y=Y[:, 1], z=elevation_smoothed, - contours_z=attr( - show=true, - usecolormap=true, - highlightcolor="limegreen", - project_z=true - ), colorscale="Viridis") - plotdata3d=[trace3D] # We add the data from the image to the plot - plotlayout3d=layout3D # we update the style of the plot to fit the image. + plotdata3d, plotlayout3d = loadSurfacePlot(imgIntT) GC.gc() # Trigger garbage collection if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS @@ -730,41 +879,7 @@ end btnSpectraDisable=true try img=load(var) - # Convert to grayscale - img_gray=Gray.(img) - img_array=Array(img_gray) - elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 - - # Smooth the image - sigma=3.0 - kernel=Kernel.gaussian(sigma) - elevation_smoothed=imfilter(elevation, kernel) - - # Create the X, Y meshgrid coordinates - x=1:size(elevation_smoothed, 2) - y=1:size(elevation_smoothed, 1) - X=repeat(reshape(x, 1, length(x)), length(y), 1) - Y=repeat(reshape(y, length(y), 1), 1, length(x)) - - layoutContour=PlotlyBase.Layout( - title="2D Topographic Map", - xaxis=PlotlyBase.attr( - title="X", - scaleanchor="y" - ), - yaxis=PlotlyBase.attr( - title="Y" - ), - ) - traceContour=PlotlyBase.contour( - z=elevation_smoothed, - x=X[1, :], # Use the first row - y=-Y[:, 1], # Use the first column - contours_coloring="Viridis", - colorscale="Viridis" - ) - plotdataC=[traceContour] - plotlayoutC=layoutContour + plotdataC,plotlayoutC=loadContourPlot(imgInt) GC.gc() # Trigger garbage collection if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS @@ -806,41 +921,7 @@ end btnSpectraDisable=true try img=load(var) - # Convert to grayscale - img_gray=Gray.(img) - img_array=Array(img_gray) - elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1 - - # Smooth the image - sigma=3.0 - kernel=Kernel.gaussian(sigma) - elevation_smoothed=imfilter(elevation, kernel) - - # Create the X, Y meshgrid coordinates - x=1:size(elevation_smoothed, 2) - y=1:size(elevation_smoothed, 1) - X=repeat(reshape(x, 1, length(x)), length(y), 1) - Y=repeat(reshape(y, length(y), 1), 1, length(x)) - - layoutContour=PlotlyBase.Layout( - title="2D Topographic Map", - xaxis=PlotlyBase.attr( - title="X", - scaleanchor="y" - ), - yaxis=PlotlyBase.attr( - title="Y" - ), - ) - traceContour=PlotlyBase.contour( - z=elevation_smoothed, - x=X[1, :], # Use the first row - y=-Y[:, 1], # Use the first column - contours_coloring="Viridis", - colorscale="Viridis" - ) - plotdataC=[traceContour] - plotlayoutC=layoutContour + plotdataC,plotlayoutC=loadContourPlot(imgIntT) GC.gc() # Trigger garbage collection if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS @@ -877,50 +958,90 @@ end # Event detection for clicking on the spectrum plot @onchange data_click begin - if !isempty(xSpectraMz) - #println("Clicked data on sum spectrum plot : ", data_click) - spectracoords=reshape(plotdata, 1, length(plotdata)) - #println("Spectra: $(ndims(spectracoords))") - # Extract x and y values from data_click - cursor_data=data_click["cursor"] - x_value = cursor_data["x"] - y_value = cursor_data["y"] # Get the x and y values from the click of the cursor - closest_distance = Inf - - for val in spectracoords - # Find the index where x is within a range - start_idx = findfirst(x -> x >= x_value - 10, val[:x]) - end_idx = findlast(x -> x <= x_value + 10, val[:x]) + if selectedTab == "tab2" + if !isempty(xSpectraMz) + #println("Clicked data on sum spectrum plot : ", data_click) + spectracoords=reshape(plotdata, 1, length(plotdata)) + #println("Spectra: $(ndims(spectracoords))") + # Extract x and y values from data_click + cursor_data=data_click["cursor"] + x_value = cursor_data["x"] + y_value = cursor_data["y"] # Get the x and y values from the click of the cursor + closest_distance = Inf - # Ensure the index are valid and within range - if start_idx !== nothing && end_idx !== nothing - for i in start_idx:end_idx - spectra_x = val[:x][i] - spectra_y = val[:y][i] - distance = sqrt((spectra_x - x_value)^2 + (spectra_y - y_value)^2) # Calculate distance - if distance < closest_distance - closest_distance = distance - Nmass = round(spectra_x, digits=2) + for val in spectracoords + # Find the index where x is within a range + start_idx = findfirst(x -> x >= x_value - 10, val[:x]) + end_idx = findlast(x -> x <= x_value + 10, val[:x]) + + # Ensure the index are valid and within range + if start_idx !== nothing && end_idx !== nothing + for i in start_idx:end_idx + spectra_x = val[:x][i] + spectra_y = val[:y][i] + distance = sqrt((spectra_x - x_value)^2 + (spectra_y - y_value)^2) # Calculate distance + if distance < closest_distance + closest_distance = distance + Nmass = round(spectra_x, digits=2) + end end end end + layoutSpectra=PlotlyBase.Layout( + title="SUM Spectrum plot", + xaxis=PlotlyBase.attr( + title="m/z", + showgrid=true + ), + yaxis=PlotlyBase.attr( + title="Intensity", + showgrid=true + ), + autosize=false + ) + traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines",name="Spectra",showlegend=false) + trace2=PlotlyBase.scatter(x=[Nmass, Nmass],y=[0, maximum(ySpectraMz)],mode="lines",line=attr(color="red", width=0.5),name="m/z selected",showlegend=false) + plotdata=[traceSpectra,trace2] # We add the data from spectra and the red line to the plot + plotlayout=layoutSpectra end - layoutSpectra=PlotlyBase.Layout( - title="SUM Spectrum plot", - xaxis=PlotlyBase.attr( - title="m/z", - showgrid=true - ), - yaxis=PlotlyBase.attr( - title="Intensity", - showgrid=true - ), - autosize=false - ) - traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines",name="Spectra",showlegend=false) - trace2=PlotlyBase.scatter(x=[Nmass, Nmass],y=[0, maximum(ySpectraMz)],mode="lines",line=attr(color="red", width=0.5),name="m/z selected",showlegend=false) - plotdata=[traceSpectra,trace2] # We add the data from spectra and the red line to the plot - plotlayout=layoutSpectra + elseif selectedTab == "tab1" + #println("you have clicked the triq image") + cursor_data=data_click["cursor"] + xCoord = Int32(round(cursor_data["x"])) + if xCoord < 0 + xCoord = 0 + elseif xCoord > imgWidth + xCoord = imgWidth + end + yCoord = Int32(round(cursor_data["y"])) + if yCoord > 0 + yCoord = 0 + elseif yCoord < -imgHeight + yCoord = -imgHeight + end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions + #plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) + plotdataImgT = filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImgT) + trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight) + plotdataImgT=append!(plotdataImgT, [trace1, trace2]) + elseif selectedTab == "tab0" + #println("you have clicked the normal image") + cursor_data=data_click["cursor"] + xCoord = Int32(round(cursor_data["x"])) + if xCoord < 0 + xCoord = 0 + elseif xCoord > imgWidth + xCoord = imgWidth + end + yCoord = Int32(round(cursor_data["y"])) + if yCoord > 0 + yCoord = 0 + elseif yCoord < -imgHeight + yCoord = -imgHeight + end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions + #plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) + plotdataImg = filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImg) + trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight) + plotdataImg=append!(plotdataImg, [trace1, trace2]) end end @@ -934,12 +1055,12 @@ end ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS end end -# ==Pages == +# == Pages == # Register a new route and the page that will be loaded on access @page("/", "app.jl.html") end -# ==Advanced features == +# == Advanced features == #= - The @private macro defines a reactive variable that is not sent to the browser. This is useful for storing data that is unique to each user session but is not needed diff --git a/app.jl.html b/app.jl.html index eadead2..b4f884b 100644 --- a/app.jl.html +++ b/app.jl.html @@ -160,7 +160,8 @@
- + +
@@ -180,7 +181,8 @@
- + +
@@ -192,8 +194,7 @@ - + @@ -246,7 +247,7 @@
- +
@@ -265,7 +266,7 @@
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@@ -301,7 +302,7 @@
- +
@@ -320,7 +321,7 @@
- +
diff --git "a/ongoing_tasks.txt\n" "b/ongoing_tasks.txt\n" index 4879e9c..94a226e 100644 --- "a/ongoing_tasks.txt\n" +++ "b/ongoing_tasks.txt\n" @@ -1,9 +1,8 @@ PENDING Rmsi & julia coherence with image creation and colorbar - colorbar revamp + colorbar revamp CURRENTLY ONGOING Create function that makes the imzML from mzML files ? Possibility to add multiple imzML to process at once ? - Per pixel of image plot creation for spectra Add comparison image (rotate, transform, translate, transparency) CURRENTLY ONGOING DONE @@ -25,3 +24,4 @@ DONE Comparative for two views Even faster initial boot and subsectuential boot Multiple spectra plot types + Plot creation for spectra Per pixel of image diff --git a/start_MSI_GUI.jl b/start_MSI_GUI.jl index 2935fa3..f23f076 100644 --- a/start_MSI_GUI.jl +++ b/start_MSI_GUI.jl @@ -37,6 +37,8 @@ Genie.loadapp() @async run(`xdg-open $url`) # For Linux elseif Sys.iswindows() @async run(`start $url`) # For Windows + @async run(`explorer $url`) + @async run(`Start-Process $url`) # For Windows end end