diff --git a/app.jl b/app.jl
index 7718948..a1c16c0 100644
--- a/app.jl
+++ b/app.jl
@@ -59,6 +59,7 @@ include("./julia_imzML_visual.jl")
@in triq3dPlot=false # To generate 3d plot based on current triq image
@in imageCPlot=false # To generate contour plots of current image
@in triqCPlot=false # To generate contour plots of current triq image
+ @in btnCreateImz=false # To start process for creating imzML and Ibd with mzML and Syncro
# Image change buttons
@in imgPlus=false
@in imgMinus=false
@@ -83,7 +84,7 @@ include("./julia_imzML_visual.jl")
@out imgIntT="/.bmp" # image Interface TrIQ
@out colorbar="/.png"
@out colorbarT="/.png"
- # interface controlling for the comparative view
+ # Interface controlling for the comparative view
@out imgIntComp="/.bmp" # image Interface
@out imgIntTComp="/.bmp" # image Interface TrIQ
@out colorbarComp="/.png"
@@ -247,10 +248,12 @@ include("./julia_imzML_visual.jl")
@onbutton btnSearch begin
full_route=pick_file(; filterlist="imzML,mzML")
- if isnothing(full_route)
+ if full_route==""
msg="No file selected"
warning_msg=true
btnStartDisable=true
+ btnSpectraDisable=true
+ SpectraEnabled=false
else
if endswith(full_route, "imzML") # Case if the file loaded is imzML
btnStartDisable=false
@@ -914,44 +917,22 @@ include("./julia_imzML_visual.jl")
CompareDialog=true
end
- # Event detection for clicking on the spectrum plot
+ @onbutton btnCreateImz begin
+ msg="Not yet implemented"
+ end
+
+ # To include a visualization in the spectrum plot indicating where is the selected mass
+ @onchange Nmass begin
+ if !isempty(xSpectraMz)
+ 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
+ end
+ end
+
+ # Event detection for clicking on the images
@onchange data_click begin
- if selectedTab == "tab2"
- if !isempty(xSpectraMz)
- spectracoords=reshape(plotdata, 1, length(plotdata))
- # Extract x and y values from data_click
- cursor_data=data_click["cursor"]
- x_value=cursor_data["x"]
- y_value=cursor_data["y"]
-
- # Find the minimum x-value in spectracoords
- min_x_value=minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
- # Adjust x_value and spectracoords x-values to start from 0
- adjusted_x_value=x_value - min_x_value
-
- closest_distance=Inf
- for val in spectracoords
- adjusted_x=val[:x] .- min_x_value
- start_idx=findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
- end_idx=findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
-
- if start_idx !== nothing && end_idx !== nothing
- for i in start_idx:end_idx
- spectra_x=adjusted_x[i]
- spectra_y=val[:y][i]
- distance=sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
- if distance < closest_distance
- closest_distance=distance
- Nmass=round(spectra_x + min_x_value, digits=2)
- end
- end
- end
- end
- 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
- end
- elseif selectedTab == "tab1"
+ if selectedTab == "tab1"
cursor_data=data_click["cursor"]
xCoord=Int32(round(cursor_data["x"]))
yCoord=Int32(round(cursor_data["y"]))
@@ -990,11 +971,11 @@ include("./julia_imzML_visual.jl")
@onbutton btnOptical begin
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
- selectedTab="tab0"
- plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
- if isnothing(imgRoute)
+ if imgRoute==""
msg="No optical image selected"
else
+ selectedTab="tab0"
+ plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
img=load(imgRoute)
save("./public/css/imgOver.png",img)
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
@@ -1004,11 +985,11 @@ include("./julia_imzML_visual.jl")
@onbutton btnOpticalT begin
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
- selectedTab="tab1"
- plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
- if isnothing(imgRoute)
+ if imgRoute==""
msg="No optical image selected"
else
+ selectedTab="tab1"
+ plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
img=load(imgRoute)
save("./public/css/imgOver.png",img)
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
@@ -1017,19 +998,19 @@ include("./julia_imzML_visual.jl")
end
@onchange imgTrans begin
- if !opticalOverTriq
+ if !opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
- else
+ elseif opticalOverTriq && imgRoute!=""
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
end
end
@onchange opticalOverTriq begin
- if !opticalOverTriq
+ if !opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
selectedTab="tab0"
- else
+ elseif opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
selectedTab="tab1"
diff --git a/app.jl.html b/app.jl.html
index 414d971..ea456c0 100644
--- a/app.jl.html
+++ b/app.jl.html
@@ -7,22 +7,21 @@
name.
It may take a while to generate the image and the plot, please be patient.
To generate the contour or surface plots, you have to select the desired image first using the interface.
+
Syncro file is required to create imzML and ibd files.
-
Search for the imzML or mzML file in your system
-
full route: {{full_route}}
-
@@ -53,8 +52,6 @@
val => triqEnabled ? ( '* Required', val >= 0.8 && val <= 1 || 'Needs to be in range between 0.8 and 1') : true
]" :readonly="!triqEnabled" :disable="!triqEnabled">