first patch to fix colorbar coherence with R
This commit is contained in:
Pixelguy14
parent
7667bc26e9
commit
e5e6284d53
217
app.jl
217
app.jl
@ -18,7 +18,6 @@ using StipplePlotly
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# == Code import ==
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# add your data analysis code here or in the lib folder. Code in lib/ will be
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# automatically loaded
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rgb_ViridisPalette=reinterpret(ColorTypes.RGB24, ViridisPalette)
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# == Search functions ==
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function increment_image(current_image, image_list)
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@ -62,50 +61,50 @@ function loadImgPlot(interfaceImg::String)
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elevation=Float32.(Array(img_gray))
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#println(typeof(elevation))
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# Get the X, Y coordinates of the image
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height, width = size(img_array)
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height, width=size(img_array)
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#println("height: $(height), width: $(width)")
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X = collect(1:width)
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Y = collect(1:height)
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X=collect(1:width)
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Y=collect(1:height)
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# Create the layout
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layout = PlotlyBase.Layout(
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xaxis = PlotlyBase.attr(
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visible = false,
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scaleanchor = "y"
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layout=PlotlyBase.Layout(
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xaxis=PlotlyBase.attr(
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visible=false,
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scaleanchor="y"
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),
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yaxis = PlotlyBase.attr(
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visible = false
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yaxis=PlotlyBase.attr(
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visible=false
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)
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)
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# Create the trace for the image
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trace = PlotlyBase.heatmap(
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z = elevation,
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x = X,
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y = -Y,
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trace=PlotlyBase.heatmap(
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z=elevation,
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x=X,
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y=-Y,
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name="",
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showlegend=false,
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colorscale = "Viridis",
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showscale = true,
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colorbar = attr(
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title = attr(
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text = "Intensity",
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font = attr(
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size = 14,
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color = "black"
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colorscale="Viridis",
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showscale=false,
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colorbar=attr(
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title=attr(
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text="Intensity",
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font=attr(
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size=14,
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color="black"
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),
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side = "right"
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side="right"
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),
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ticks = "outside",
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ticklen = 2,
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tickwidth = 0.5,
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nticks = 5,
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tickformat = ".2g"
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ticks="outside",
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ticklen=2,
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tickwidth=0.5,
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nticks=5,
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tickformat=".2g"
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)
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)
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plotdata = [trace]
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plotlayout = layout
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plotdata=[trace]
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plotlayout=layout
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return plotdata, plotlayout, width, height
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end
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# loadContourPlot recieves the local directory of the image as a string,
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@ -149,12 +148,12 @@ function loadContourPlot(interfaceImg::String)
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y=-Y[:, 1], # Use the first column
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contours_coloring="Viridis",
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colorscale="Viridis",
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colorbar = attr(
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tickformat = ".2g"
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colorbar=attr(
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tickformat=".2g"
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)
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)
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plotdata = [trace]
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plotlayout = layout
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plotdata=[trace]
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plotlayout=layout
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return plotdata, plotlayout
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end
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# loadSurfacePlot recieves the local directory of the image as a string,
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@ -220,25 +219,25 @@ function loadSurfacePlot(interfaceImg::String)
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project_z=true
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),
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colorscale="Viridis",
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colorbar = attr(
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tickformat = ".2g"
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colorbar=attr(
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tickformat=".2g"
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)
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)
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plotdata = [trace3D]
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plotlayout = layout3D
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plotdata=[trace3D]
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plotlayout=layout3D
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return plotdata, plotlayout
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end
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function crossLinesPlot(x, y, maxwidth, maxheight)
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# Define the coordinates for the two lines
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l1_x = [0, maxwidth]
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l1_y = [y, y]
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l2_x = [x, x]
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l2_y = [0, maxheight]
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l1_x=[0, maxwidth]
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l1_y=[y, y]
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l2_x=[x, x]
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l2_y=[0, maxheight]
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# Create the line traces
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trace1 = PlotlyBase.scatter(x = l1_x, y = l1_y, mode = "lines",line=attr(color="red", width=0.5),name="Line X",showlegend=false)
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trace2 = PlotlyBase.scatter(x = l2_x, y = l2_y, mode = "lines",line=attr(color="red", width=0.5),name="Line Y",showlegend=false)
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trace1=PlotlyBase.scatter(x=l1_x, y=l1_y, mode="lines",line=attr(color="red", width=0.5),name="Line X",showlegend=false)
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trace2=PlotlyBase.scatter(x=l2_x, y=l2_y, mode="lines",line=attr(color="red", width=0.5),name="Line Y",showlegend=false)
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return trace1, trace2
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end
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@ -272,9 +271,9 @@ end
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@in file_route=""
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@in file_name=""
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@in Nmass=0.0
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@in Tol=0.0
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@in Tol=0.1
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@in triqProb=0.98
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@in triqColor=256
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@in colorLevel=20
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## Interface Buttons
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@in btnSearch=false # To search for files in your device
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@ -340,21 +339,21 @@ end
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## Plots
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# Local image to plot
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layoutImg = PlotlyBase.Layout(
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xaxis = PlotlyBase.attr(
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visible = false,
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scaleanchor = "y"
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layoutImg=PlotlyBase.Layout(
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xaxis=PlotlyBase.attr(
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visible=false,
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scaleanchor="y"
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),
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yaxis = PlotlyBase.attr(
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visible = false
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yaxis=PlotlyBase.attr(
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visible=false
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)
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)
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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@out plotdataImg = [traceImg]
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@out plotlayoutImg = layoutImg
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@out plotdataImg=[traceImg]
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@out plotlayoutImg=layoutImg
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# For triq image
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@out plotdataImgT = [traceImg]
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@out plotlayoutImgT = layoutImg
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@out plotdataImgT=[traceImg]
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@out plotlayoutImgT=layoutImg
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# Interface Plot Spectrum
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layoutSpectra=PlotlyBase.Layout(
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title="SUM Spectrum plot",
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@ -475,12 +474,12 @@ end
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# Append a query string to force the image to refresh
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timestamp=string(time_ns())
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if triqEnabled # If we have TrIQ
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if triqColor < 1 || triqColor > 256 ||triqProb < 0 || triqProb > 1
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if colorLevel < 2 || colorLevel > 256 ||triqProb < 0.8 || triqProb > 1
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msg="Incorrect TrIQ values, please adjust accordingly and try again."
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warning_msg=true
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else
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image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
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SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(triqColor), triqProb),ViridisPalette)
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SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(colorLevel), triqProb),ViridisPalette)
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# Flip te image vertically then save it again
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img=load(image_path)
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if size(img, 1) > size(img, 2) # fix to taller images
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@ -492,13 +491,17 @@ end
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save(image_path, flipped_img)
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# Use timestamp to refresh image interface container
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imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT)
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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# Get current image
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current_triq="TrIQ_$(text_nmass).bmp"
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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ticks=round.(range(0, stop=maximum(TrIQ(slice, Int(triqColor), triqProb)), length=10), sigdigits=3)
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Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(triqColor), triqProb))),ticks=ticks, label="Intensity")
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#ticks=round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3)
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#println("ticks: $(round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3))")
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ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3)
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#println("ticks 2: $(round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3))")
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#Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(colorLevel), triqProb))),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity")
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save("public/colorbar_TrIQ_$(text_nmass).png", fig)
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colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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@ -527,13 +530,15 @@ end
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save(image_path, flipped_img)
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# Use timestamp to refresh image interface container
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imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)"
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plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt)
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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# Get current image
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current_msi="MSI_$(text_nmass).bmp"
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
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Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
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#ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
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ticks=round.(range(0, stop=maximum(slice), length=15), sigdigits=3)
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#Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, 256, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
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save("public/colorbar_MSI_$(text_nmass).png", fig)
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colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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@ -694,11 +699,11 @@ end
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt)
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImg = [traceImg]
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msgimg = ""
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plotdataImg=[traceImg]
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msgimg=""
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end
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end
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@onbutton imgPlus begin
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@ -720,11 +725,11 @@ end
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt)
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImg = [traceImg]
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msgimg = ""
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plotdataImg=[traceImg]
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msgimg=""
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end
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end
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@ -747,11 +752,11 @@ end
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT)
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgT = [traceImg]
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msgtriq = ""
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plotdataImgT=[traceImg]
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msgtriq=""
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end
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end
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@onbutton imgPlusT begin
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@ -773,11 +778,11 @@ end
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT)
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgT = [traceImg]
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msgtriq = ""
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plotdataImgT=[traceImg]
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msgtriq=""
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end
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end
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@ -795,7 +800,7 @@ end
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btnStartDisable=true
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btnSpectraDisable=true
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try
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plotdata3d, plotlayout3d = loadSurfacePlot(imgInt)
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plotdata3d, plotlayout3d=loadSurfacePlot(imgInt)
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GC.gc() # Trigger garbage collection
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if Sys.islinux()
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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@ -836,7 +841,7 @@ end
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btnStartDisable=true
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btnSpectraDisable=true
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try
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plotdata3d, plotlayout3d = loadSurfacePlot(imgIntT)
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plotdata3d, plotlayout3d=loadSurfacePlot(imgIntT)
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GC.gc() # Trigger garbage collection
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if Sys.islinux()
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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@ -965,24 +970,24 @@ end
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#println("Spectra: $(ndims(spectracoords))")
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# Extract x and y values from data_click
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cursor_data=data_click["cursor"]
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x_value = cursor_data["x"]
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y_value = cursor_data["y"] # Get the x and y values from the click of the cursor
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closest_distance = Inf
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x_value=cursor_data["x"]
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y_value=cursor_data["y"] # Get the x and y values from the click of the cursor
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closest_distance=Inf
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for val in spectracoords
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# Find the index where x is within a range
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start_idx = findfirst(x -> x >= x_value - 10, val[:x])
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end_idx = findlast(x -> x <= x_value + 10, val[:x])
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start_idx=findfirst(x -> x >= x_value - 10, val[:x])
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end_idx=findlast(x -> x <= x_value + 10, val[:x])
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# Ensure the index are valid and within range
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if start_idx !== nothing && end_idx !== nothing
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for i in start_idx:end_idx
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spectra_x = val[:x][i]
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spectra_y = val[:y][i]
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distance = sqrt((spectra_x - x_value)^2 + (spectra_y - y_value)^2) # Calculate distance
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spectra_x=val[:x][i]
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spectra_y=val[:y][i]
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distance=sqrt((spectra_x - x_value)^2 + (spectra_y - y_value)^2) # Calculate distance
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if distance < closest_distance
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closest_distance = distance
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Nmass = round(spectra_x, digits=2)
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closest_distance=distance
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Nmass=round(spectra_x, digits=2)
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end
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end
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end
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@ -1007,40 +1012,40 @@ end
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elseif selectedTab == "tab1"
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#println("you have clicked the triq image")
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cursor_data=data_click["cursor"]
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xCoord = Int32(round(cursor_data["x"]))
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xCoord=Int32(round(cursor_data["x"]))
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if xCoord < 0
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xCoord = 0
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xCoord=0
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elseif xCoord > imgWidth
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xCoord = imgWidth
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xCoord=imgWidth
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end
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yCoord = Int32(round(cursor_data["y"]))
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yCoord=Int32(round(cursor_data["y"]))
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if yCoord > 0
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yCoord = 0
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yCoord=0
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elseif yCoord < -imgHeight
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yCoord = -imgHeight
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yCoord=-imgHeight
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end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions
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#plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT)
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plotdataImgT = filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImgT)
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trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
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#plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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plotdataImgT=filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImgT)
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trace1, trace2=crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
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plotdataImgT=append!(plotdataImgT, [trace1, trace2])
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elseif selectedTab == "tab0"
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#println("you have clicked the normal image")
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cursor_data=data_click["cursor"]
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xCoord = Int32(round(cursor_data["x"]))
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xCoord=Int32(round(cursor_data["x"]))
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if xCoord < 0
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xCoord = 0
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xCoord=0
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elseif xCoord > imgWidth
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xCoord = imgWidth
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xCoord=imgWidth
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end
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yCoord = Int32(round(cursor_data["y"]))
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yCoord=Int32(round(cursor_data["y"]))
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if yCoord > 0
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yCoord = 0
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yCoord=0
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elseif yCoord < -imgHeight
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yCoord = -imgHeight
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yCoord=-imgHeight
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end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions
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#plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt)
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plotdataImg = filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImg)
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trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
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#plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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plotdataImg=filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImg)
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trace1, trace2=crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
|
||||
plotdataImg=append!(plotdataImg, [trace1, trace2])
|
||||
end
|
||||
end
|
||||
|
||||
12
app.jl.html
12
app.jl.html
@ -60,10 +60,10 @@
|
||||
<div class="st-col col-12 col-sm q-ma-sm">
|
||||
<q-input standout="custom-standout" id="textNmass" step="0.01" v-model="Nmass"
|
||||
label="Mass-to-charge ratio of interest" type="number"
|
||||
:rules="[ val => !!val || '* Required', val => val >= 0.0 && val <= 2000.0 || 'Need positive mass values',]"></q-input>
|
||||
:rules="[ val => !!val || '* Required', val => val >= 0.0 || 'Need positive mass values',]"></q-input>
|
||||
</div>
|
||||
<div class="st-col col-12 col-sm q-ma-sm">
|
||||
<q-input standout="custom-standout" id="textTol" step="0.01" v-model="Tol"
|
||||
<q-input standout="custom-standout" id="textTol" step="0.05" v-model="Tol"
|
||||
label="Mass-to-charge ratio tolerance" type="number"
|
||||
:rules="[val => !!val || '* Required', val => val >= 0.0 && val <= 1.0 || 'Needs to be in range between 0 and 1',]"></q-input>
|
||||
</div>
|
||||
@ -73,19 +73,19 @@
|
||||
<div class="col-6">
|
||||
<div class="st-col col-6 col-sm q-ma-sm">
|
||||
<q-toggle id="btnEnableTriq" v-on:click="triqEnabled" v-model="triqEnabled" color="blue"
|
||||
label="Add Threshold Intensity Quantization (TrIQ)!"></q-toggle>
|
||||
label="Add Threshold Intensity Quantization (TrIQ)"></q-toggle>
|
||||
</div>
|
||||
<div class="row">
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<q-input standout="custom-standout" id="textTriqProb" step="0.01" v-model="triqProb"
|
||||
label="TrIQ probability" type="number" :rules="[
|
||||
val => triqEnabled ? ( '* Required', val >= 0 && val <= 1 || 'Needs to be in range between 0 and 1') : true
|
||||
val => triqEnabled ? ( '* Required', val >= 0.8 && val <= 1 || 'Needs to be in range between 0.8 and 1') : true
|
||||
]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
|
||||
</div>
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<q-input standout="custom-standout" id="textTriqColor" step="1" v-model="triqColor"
|
||||
<q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
|
||||
label="TrIQ color levels" type="number" :rules="[
|
||||
val => triqEnabled ? ( '* Required', val >= 0 && val <= 256 || 'Needs to be in range between 1 and 256') : true
|
||||
val => triqEnabled ? ( '* Required', val >= 2 && val <= 256 || 'Needs to be in range between 2 and 256') : true
|
||||
]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user