--- a/marea_2/flux_to_map.py	Sun Aug 04 17:59:54 2024 +0000
+++ b/marea_2/flux_to_map.py	Sun Aug 04 18:09:33 2024 +0000
@@ -814,23 +814,24 @@
     dataset = dataset.drop(dataset.columns[0], axis = "columns").to_dict("list")
     return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs
 
-def rgba_to_hex(rgba):
-    """Convert an RGBA color to HEX format including alpha."""
-    return '#{:02x}{:02x}{:02x}{:02x}'.format(int(rgba[0] * 255), int(rgba[1] * 255), int(rgba[2] * 255), int(rgba[3] * 255))
-
-def gray_to_red_cmap(value):
+def jet_colormap(value):
+    # Ensure value is a single numeric value
     value = abs(value)
+    
+    # Define the red, green, and blue color components
+    red = np.clip(1.5 - np.abs(4 * (value - 0.75)), 0, 1)
+    green = np.clip(1.5 - np.abs(4 * (value - 0.5)), 0, 1)
+    blue = np.clip(1.5 - np.abs(4 * (value - 0.25)), 0, 1)
+    
+    # Combine the color components into an RGB array
+    rgb = np.array([red, green, blue])
+    
+    return rgb
 
-    # Red color (1, 0, 0)
-    r = 1
-    g = 0
-    b = 0
-    
-    # Log scale for opacity transition from 0.5 to 1
-    log_value = math.log10(1 + 9 * value) / math.log10(10)  # Log scale from 0 to 1
-    alpha = 0.5 + 0.5 * log_value
-    
-    return (r, g, b, alpha)
+def rgb_to_hex(rgb):
+    # Convert RGB values (0-1 range) to hexadecimal format
+    rgb = (rgb * 255).astype(int)
+    return '#{:02x}{:02x}{:02x}'.format(rgb[0], rgb[1], rgb[2])
     
 
 def computeEnrichmentMeanMedian(metabMap :ET.ElementTree, class_pat :Dict[str, List[List[float]]], ids :List[str]) -> None:
@@ -861,48 +862,28 @@
         colors_median={}
         i=0
         for rxn_id in ids:
-             colors_median[rxn_id] = rgba_to_hex(gray_to_red_cmap(medians[key][i]))
+             colors_median[rxn_id] = rgb_to_hex(jet_colormap(medians[key][i]))
              i+=1
 
         colors_mean={}
         i=0
         for rxn_id in ids:
-             colors_mean[rxn_id] = rgba_to_hex(gray_to_red_cmap(means[key][i]))
+             colors_mean[rxn_id] = rgb_to_hex(jet_colormap(means[key][i]))
              i+=1
 
         for rxn_id in ids:
             arrow = Arrow(width=5, col=colors_median[rxn_id])
-            #arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_median, arrow.toStyleStr())
-            #arrow.applyTo(getArrowBodyElementId(rxn_id), metabMap_median, arrow.toStyleStr())
             arrow.styleReactionElements(metabMap_median, rxn_id, mindReactionDir=False)
-
             idOpt1, idOpt2 = getArrowHeadElementId(rxn_id)
             arrow.applyTo(idOpt1, metabMap_median, arrow.toStyleStr(downSizedForTips = True))
             if idOpt2: arrow.applyTo(idOpt2, metabMap_median, arrow.toStyleStr(downSizedForTips = True))
 
-            # Now we style the arrow head(s):
-            #idOpt1, idOpt2 = getArrowHeadElementId(arrow.getMapReactionId(rxn_id, mindReactionDir=True))
-            #arrow.applyTo(idOpt1, metabMap_median, arrow.toStyleStr(downSizedForTips = True))
-            #if idOpt2: arrow.applyTo(idOpt2, metabMap_median, arrow.toStyleStr(downSizedForTips = True))
-            #arrow = Arrow(width=5, col="#00FF00")
-            #arrow.styleReactionElements(metabMap_median, arrow.getMapReactionId(rxn_id, mindReactionDir=False), mindReactionDir=False)
-
             arrow = Arrow(width=5, col=colors_mean[rxn_id])
-            #arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_mean, arrow.toStyleStr())
-            #arrow.applyTo(getArrowBodyElementId(rxn_id), metabMap_mean, arrow.toStyleStr())
             arrow.styleReactionElements(metabMap_mean, rxn_id, mindReactionDir=False)
-
             idOpt1, idOpt2 = getArrowHeadElementId(rxn_id)
             arrow.applyTo(idOpt1, metabMap_mean, arrow.toStyleStr(downSizedForTips = True))
             if idOpt2: arrow.applyTo(idOpt2, metabMap_mean, arrow.toStyleStr(downSizedForTips = True))
 
-            # Now we style the arrow head(s):
-            #idOpt1, idOpt2 = getArrowHeadElementId(arrow.getMapReactionId(rxn_id, mindReactionDir=True))
-            #arrow.applyTo(idOpt1, metabMap_mean, arrow.toStyleStr(downSizedForTips = True))
-            #if idOpt2: arrow.applyTo(idOpt2, metabMap_mean, arrow.toStyleStr(downSizedForTips = True))
-            #arrow = Arrow(width=5, col="#00FF00")
-            #arrow.styleReactionElements(metabMap_mean, arrow.getMapReactionId(rxn_id, mindReactionDir=False), mindReactionDir=False)
-
         svgFilePath = utils.FilePath("SVG Map mean - " + str(key), ext = utils.FileFormat.SVG, prefix="result")
         utils.writeSvg(svgFilePath, metabMap_mean)