From 8e1c473acbdb74d02af8022efb55e9f71248069c Mon Sep 17 00:00:00 2001
From: Pixelguy14 <pixelguy14@gmail.com>
Date: Sun, 9 Mar 2025 14:02:53 -0600
Subject: [PATCH] median filter border fix, files get renamed if they don't
 have correct extension

---
 app.jl                | 50 ++++++++++++++++++++++++++++++++-----------
 julia_imzML_visual.jl | 28 +++++++++++++++++++-----
 2 files changed, 60 insertions(+), 18 deletions(-)

diff --git a/app.jl b/app.jl
index beaa226..9c0255f 100644
--- a/app.jl
+++ b/app.jl
@@ -13,6 +13,7 @@ using Images
 using LinearAlgebra
 using NativeFileDialog # Opens the file explorer depending on the OS
 using StipplePlotly
+using Base.Filesystem: mv # To rename files in the system
 include("./julia_imzML_visual.jl")
 @genietools
 
@@ -248,8 +249,34 @@ include("./julia_imzML_visual.jl")
     # The onbutton handler will set the variable to false after the block is executed
 
     @onbutton btnSearch begin
-        full_route=pick_file(; filterlist="imzML,mzML")
+        full_route=pick_file(; filterlist="imzML,imzml,mzML,mzml")
         msg=""
+        if full_route != ""
+            if endswith(full_route, "imzml")
+                alt_route=replace(full_route, r"\.[^.]*$" => ".imzML")
+                mv(full_route, alt_route)
+                full_route=alt_route
+                # to detect if there's an mzml named wrong
+                alt_routeMz=replace(full_route, r"\.[^.]*$" => ".mzml") 
+                if isfile(alt_routeMz)
+                    alt_routeMz2=replace(alt_routeMz, r"\.[^.]*$" => ".mzML") 
+                    mv(alt_routeMz, alt_routeMz2)
+                    alt_routeMz=alt_routeMz2
+                end
+            end
+            if endswith(full_route, "mzml")
+                alt_route=replace(full_route, r"\.[^.]*$" => ".mzML") 
+                mv(full_route, alt_route)
+                full_route = alt_route 
+                # to detect if there's an imzml named wrong
+                alt_routeMz=replace(full_route, r"\.[^.]*$" => ".imzml") 
+                if isfile(alt_routeMz)
+                    alt_routeMz2=replace(alt_routeMz, r"\.[^.]*$" => ".imzML") 
+                    mv(alt_routeMz, alt_routeMz2)
+                    alt_routeMz=alt_routeMz2
+                end
+            end
+        end
         if full_route==""
             msg="No file selected"
             warning_msg=true
@@ -283,7 +310,7 @@ include("./julia_imzML_visual.jl")
                     eTime=round(fTime-sTime,digits=3)
                     msg="Plot loaded in $(eTime) seconds"
                 else
-                    # If there's no MzML file, we deny access again
+                    # If there's no mzML file, we deny access again
                     btnSpectraDisable=true
                     SpectraEnabled=false
                 end
@@ -291,17 +318,6 @@ include("./julia_imzML_visual.jl")
                 full_routeMz=full_route
                 btnSpectraDisable=false
                 SpectraEnabled=true
-                # Splitting the route the same way
-                full_route=replace(full_route, r"\.[^.]*$" => ".imzML")
-                if isfile(full_route)
-                    btnStartDisable=false
-                else
-                    btnStartDisable=true
-                    full_route=full_routeMz
-                end
-                if endswith(full_route, "imzML")
-                    btnStartDisable=false
-                end
                 if isfile(full_routeMz)
                     # Start the sum spectrum creation on loading
                     progressSpectraPlot=true
@@ -322,6 +338,14 @@ include("./julia_imzML_visual.jl")
                     eTime=round(fTime-sTime,digits=3)
                     msg="Plot loaded in $(eTime) seconds"
                 end
+                # Splitting the route the same way
+                full_route=replace(full_route, r"\.[^.]*$" => ".imzML")
+                if isfile(full_route)
+                    btnStartDisable=false
+                else
+                    btnStartDisable=true
+                    full_route=full_routeMz
+                end
             end
             xCoord=0
             yCoord=0
diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl
index 7c5add6..2316c25 100644
--- a/julia_imzML_visual.jl
+++ b/julia_imzML_visual.jl
@@ -409,21 +409,39 @@ end
 # This one in particular is a midpoint fiter from a 3x3 neighbour area
 function medianFilterjl(pixMap)
     height, width = size(pixMap)
+    padded_pixMap = padarray(pixMap, 1)
     target = zeros(eltype(pixMap), height, width)
-    for j in 2:(width-1)
-        for i in 2:(height-1)
+    
+    for j in 1:width
+        for i in 1:height
             neighbors = []
-            for dj in max(1, j-1):min(j+1, width)
-                for di in max(1, i-1):min(i+1, height)
-                    push!(neighbors, pixMap[di, dj])
+            for dj in j:j+2
+                for di in i:i+2
+                    push!(neighbors, padded_pixMap[di, dj])
                 end
             end
             target[i, j] = median(neighbors)
         end
     end
+    
     return target
 end
 
+function padarray(A, padsize)
+    h, w = size(A)
+    padded = zeros(eltype(A), h + 2*padsize, w + 2*padsize)
+    padded[padsize+1:end-padsize, padsize+1:end-padsize] .= A
+    padded[1:padsize, padsize+1:end-padsize] .= A[1:padsize, :]
+    padded[end-padsize+1:end, padsize+1:end-padsize] .= A[end-padsize+1:end, :]
+    padded[padsize+1:end-padsize, 1:padsize] .= A[:, 1:padsize]
+    padded[padsize+1:end-padsize, end-padsize+1:end] .= A[:, end-padsize+1:end]
+    padded[1:padsize, 1:padsize] .= A[1, 1]
+    padded[1:padsize, end-padsize+1:end] .= A[1, end]
+    padded[end-padsize+1:end, 1:padsize] .= A[end, 1]
+    padded[end-padsize+1:end, end-padsize+1:end] .= A[end, end]
+    return padded
+end
+
 # sumSpectrumPlot recieves the local directory of the image as a string,
 # returns the layout and data for the surface plotly plot
 # this function loads the spectra data and makes a mean to display