Added files for conversion of coordinates

miscellaneous/convertJSON2TXT.py

@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Jul 20 15:39:23 2022
+
+Script to convert meshview compatible JSON files to TXT file using the same colour definitions.
+Text files are saved in the same folder as the original JSON files using the same file names.
+
+This script was written for a specific set of files, but works for all meshview compatible JSON files 
+as long as the folder the JSON files are stored in is correctly defined. This can be changed by modifying 
+the definition of the variable "fnames".
+
+@author: mvanswieten
+"""
+
+import os
+import json
+import glob
+
+fpath = os.getcwd()
+
+# Find all JSON files that are in the subfolders of the folders in the directory
+fnames = glob.glob(fpath + "**\\**\\*.json", recursive = True)
+
+# Open the files and add them to a list for further processing
+file_list = []
+for fname in fnames:
+    with open(fname, 'r') as f:
+        file_list.append(json.load(f))
+    f.close()
+
+# Loop over the list and process each file individually
+for i in range(len(file_list)):
+    exp_name = fnames[i].split("\\")[-1].split(".json")[0].split("_")[0:1]
+    output_folder = "\\".join(fnames[i].split("\\")[:-1])
+    print("Loading data for experiment: " + exp_name[i])
+    # Extract the x, y, z coordinates for the list of "triplets". 
+    for f in file_list[i]:
+
+        coordinate_list = f["triplets"]
+
+        fname_txt = f["name"] + ".txt"
+        xs = coordinate_list[0::3]
+        ys = coordinate_list[1::3]
+        zs = coordinate_list[2::3]
+        with open(os.path.join(output_folder,fname_txt), 'w') as fi:
+            fi.write("RGB " + str(f["r"]) + " " + str(f["g"]) + " " + str(f["b"]))
+            fi.write('\n')
+            for l in range(f["count"]):
+                fi.write(str(xs[l]))
+                fi.write('\t')
+                fi.write(str(ys[l]))
+                fi.write('\t')
+                fi.write(str(zs[l]))
+                fi.write('\n')

miscellaneous/convertXYZ2JSON.py

@@ -0,0 +1,93 @@
+"""
+Created on Jul 20 13:52:25 2022
+
+Script to convert coordinates from a .xyz file to a JSON file compatible with Meshview
+
+This script was written for a specific set of files, but works for all .xyz files as long 
+as the folder the .xyz files are stored in is correctly defined. This can be changed by modifying 
+the definition of the variable "experiment_files". 
+
+The colour used for the JSON file is dependent on the type of injection tracer. BDA/PHA/WGA is 
+black, Fe/FE is green, Fr is red, FG is yellow, and FB is blue. If the files do not follow the 
+naming convention of the files the script was written for, then the colour of the points is set 
+to black by default.
+
+@author: mvanswieten
+"""
+
+import json
+import glob
+import os
+
+cwd = os.getcwd()
+
+# Find all JSON files that are in the subfolders of the folders in the directory
+experiment_files = glob.glob(os.path.join(cwd,"") + "**\\**\\*.xyz", recursive = True)
+
+output_path = os.path.join(cwd,"output_files")
+
+for f in range(len(experiment_files)):
+
+    triplets = []
+    with open(experiment_files[f], "r") as my_file:
+        output_folder = os.path.join(output_path, "\\".join(experiment_files[f].split("\\")[-3:-1]), "")
+        if not os.path.isdir(output_folder):
+            os.makedirs(output_folder)
+
+        if experiment_files[f].split("\\")[-2] in ["BDA", "PHA", "WGA"]:
+                r = 0
+                g = 0
+                b = 0
+        elif experiment_files[f].split("\\")[-2] in ["Fe", "FE"]:
+                r = 0
+                g = 0.5
+                b = 0
+        elif experiment_files[f].split("\\")[-2] == "Fr" :
+                r = 1
+                g = 0
+                b = 0
+        elif experiment_files[f].split("\\")[-2] == "FG":
+                r = 1
+                g = 1
+                b = 0
+        elif experiment_files[f].split("\\")[-2] == "FB":
+                r = 0
+                g = 0
+                b = 1
+        else:
+                r = 0
+                g = 0
+                b = 0
+
+        for line in my_file:
+
+            # Skip the lines with a hashtag
+            if "#" in line: 
+                continue
+            # Only consider lines that have text/coordinates on them
+            elif not line == "\n":
+                currentline = line.split(",")
+                if len(currentline[0].split(" ")) == 3:
+                    coordinates = currentline[0].split(" ")
+                else:
+                    coordinates = currentline[0].split("\t")
+
+                triplets.append(float(coordinates[0]))
+                triplets.append(float(coordinates[1]))   
+                triplets.append(float(coordinates[2].split("\n")[0]))
+
+        fname = os.path.split(experiment_files[f])[-1].split(".xyz")[0]
+        instance = {
+            "idx": 0,
+            "count": int(len(triplets)/3),
+            "r": int(r*255),
+            "g": int(g*255),
+            "b": int(b*255),
+            "name": ("_").join(fname.split("_")[2:4]),
+            "triplets": triplets
+            }
+
+        # Save the file using the original name and organisation in a new output folder
+        filename = ("_").join(fname.split("_")[2:4]) + ".json"
+        with open(os.path.join(output_folder,filename), 'w', encoding='utf-8') as fi:
+            fi.write(json.dumps([instance], ensure_ascii=False, indent=4))