Change the path to save temperature bound json file

.github/workflows/python.yml

@@ -3,7 +3,7 @@ name: Python application
 on:
   workflow_dispatch:
   pull_request:
-    types: [ labeled ]
+    types: [labeled]
 
 permissions:
   contents: read
@@ -15,19 +15,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.10"
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-    - name: Lint with flake8
-      run: |
-        flake8 . --count --show-source --statistics
-    - run: pip install -e .
-    - name: Test with unittest
-      run: |
-        python -m unittest discover tests
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+      - name: Clone Flir extractor
+        run: |
+          git clone https://github.com/ITVRoC/FlirImageExtractor.git --depth 1
+          sudo apt install exiftool python-setuptools
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --show-source --statistics --exclude FlirImageExtractor/
+      - run: pip install -e .
+      - name: Test with unittest
+        run: |
+          python -m unittest discover tests

tests/test_process_thermal.py

@@ -0,0 +1,72 @@
+import shutil
+import unittest
+from pathlib import Path
+
+from thermo_scenes.flir_thermal_images.custom_flir import CustomFlir
+
+
+class TestThermalConversion(unittest.TestCase):
+    def test_process_thermal(self) -> None:
+        """
+        Test of extracting RGB, thermal and csv files from the given msx images.
+
+        2 msx images will generate 2 RGB PNG files, 2 thermal PNG files, 2 csv files
+        and 1 temperature_bound.json file.
+        """
+        msx_path = Path("tests/data/process_thermal/msx")
+        output_path = Path("tests/data/process_thermal/output")
+
+        output_path.mkdir(exist_ok=True, parents=True)
+        shutil.rmtree(output_path)
+        output_path.mkdir(exist_ok=True, parents=True)
+
+        CustomFlir(path_to_msx_images=msx_path, path_to_output_folder=output_path)
+
+        json_count = 0
+        PNG_count = 0
+        csv_count = 0
+
+        for folder in output_path.iterdir():
+            if folder.suffix == ".json":
+                json_count += 1
+                continue
+            for files in folder.iterdir():
+                if files.suffix in [".png", ".PNG", ".jpg", ".jpeg"]:
+                    PNG_count += 1
+                elif files.suffix == ".csv":
+                    csv_count += 1
+
+        self.assertEqual(json_count, 1, "The number of the JSON file is not correct!")
+        self.assertEqual(PNG_count, 4, "The number of the PNG files is not correct!")
+        self.assertEqual(csv_count, 2, "The number of the CSV files is not correct!")
+
+    def test_name_consistency(self) -> None:
+        """
+        Test the name consistency of extracting RGB, thermal and csv files from the
+        given msx images.
+
+        RGB image, thermal image and csv file should have the same stem as the extracted
+        msx image.
+        """
+        msx_path = Path("tests/data/process_thermal/msx")
+        output_path = Path("tests/data/process_thermal/output")
+
+        output_path.mkdir(exist_ok=True, parents=True)
+        shutil.rmtree(output_path)
+        output_path.mkdir(exist_ok=True, parents=True)
+
+        CustomFlir(path_to_msx_images=msx_path, path_to_output_folder=output_path)
+
+        for folder in output_path.iterdir():
+            if folder.suffix == ".json":
+                continue
+            namelist = [file.stem for file in msx_path.iterdir()]
+            for files in folder.iterdir():
+                if files.stem in namelist:
+                    namelist.remove(files.stem)
+            self.assertEqual(
+                len(namelist),
+                0,
+                "Names of the extracted files are not consistent with the "
+                + "given msx images!",
+            )

thermo_scenes/docs/Collect_new_dataset.md

@@ -47,10 +47,10 @@ sudo pip install numpy matplotlib pillow
 ### Extact raw data
 
 To create the CSV files, rgb images, and the greyscale raw temperature images, run
-the following command, with `<path_to_thermal>` the path to the MSX images, and `<path_to_output_thermal>`, `<path_to_csv>`, and `<path_to_rgb>` the paths where the temperature and rgb images, and csv files extracted will be saved.
+the following command, with `<path_to_thermal>` the path to the MSX images, and `<path_to_output_folder>` the path where the temperature and rgb images, and csv files extracted will be saved.
 
 ```bash
-thermoscenes_preprocess_thermal.py --path-to-thermal-images <path_to_thermal> --path-to-thermal-images-curated <path_to_output_thermal> --path-to-rgb <path_to_rgb> --path-to-csv-files  <path_to_csv>
+thermoscenes_preprocess_thermal.py --path-to-thermal-images <path_to_thermal> --path-to-output-folder <path_to_output_folder>
 ```
 
 > If your MSX images are in more than one folder, do it for all folders, and make sure that the temperature are rescaled to the same range in the next step.

thermo_scenes/flir_thermal_images/custom_flir.py

@@ -1,4 +1,5 @@
 import json
+import shutil
 from pathlib import Path
 
 import numpy as np
@@ -47,11 +48,41 @@ class CustomFlir(FlirImageExtractor):
     in the dataset.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, path_to_msx_images: Path, path_to_output_folder: Path) -> None:
         super().__init__()
+
+        path_to_output_folder.mkdir(exist_ok=True, parents=True)
+        if path_to_msx_images != path_to_output_folder:
+            shutil.copytree(
+                path_to_msx_images,
+                Path(path_to_output_folder, "msx"),
+                dirs_exist_ok=True,
+            )
+
+        output_json_path = Path(path_to_output_folder, "temperature_bounds.json")
+
+        output_rgb_folder = Path(path_to_output_folder, "rgb")
+        output_rgb_folder.mkdir(parents=True, exist_ok=True)
+
+        output_thermal_folder = Path(path_to_output_folder, "thermal")
+        output_thermal_folder.mkdir(parents=True, exist_ok=True)
+
+        output_csv_folder = Path(path_to_output_folder, "csv")
+        output_csv_folder.mkdir(parents=True, exist_ok=True)
+
         self.absolute_max_temperature = None
         self.absolute_min_temperature = None
 
+        for img_path in path_to_msx_images.iterdir():
+            self.process_image(Path(path_to_msx_images, img_path.name))
+            self.export_thermal_to_csv(Path(output_csv_folder, img_path.stem + ".csv"))
+            self.save_rgb_images(output_rgb_folder)
+
+        self.save_normalised_thermal_images(
+            str(output_thermal_folder), str(output_csv_folder)
+        )
+        self.save_temperature_bounds(str(output_json_path))
+
     def save_rgb_images(self, path_to_rgb: Path) -> None:
         """
         Save the extracted rgb images only in the `path_to_rgb` directory.
@@ -60,9 +91,7 @@ def save_rgb_images(self, path_to_rgb: Path) -> None:
 
         img_visual = Image.fromarray(rgb_np)
 
-        fn_prefix = Path(self.flir_img_filename).name
-
-        image_filename = Path(path_to_rgb, str(fn_prefix).split(".")[0] + ".PNG")
+        image_filename = Path(path_to_rgb, Path(self.flir_img_filename).stem + ".PNG")
 
         img_visual.save(image_filename)
 
@@ -132,7 +161,7 @@ def save_normalised_coloured_thermal_images(
             )
 
             thermal_filename = Path(
-                path_to_thermal_images_curated, str(filename).split(".")[0] + ".PNG"
+                path_to_thermal_images_curated, Path(filename).stem + ".PNG"
             )
 
             img_thermal.save(str(thermal_filename))

thermo_scenes/scripts/preprocess_thermal.py

@@ -8,36 +8,19 @@
 
 @dataclass
 class Paths:
-    path_to_thermal_images: str
+    path_to_msx_images: Path
     """Path to the thermal data extracted from Flir One App."""
-    path_to_thermal_images_curated: str
-    """Path to the output thermal images created using raw thermal data."""
-    path_to_rgb: str
-    """Path to the output rgb images"""
-    path_to_csv_files: str
-    """Path to the output csv files of temperature values"""
-    path_to_txt: str = "temperature_bounds.json"
-    """Path to the txt file with temperature bounds for the dataset"""
+    path_to_output_folder: Path
+    """Path to the output folder"""
 
 
 def main() -> None:
     paths = tyro.cli(Paths)
-    list_thermal = []
-    list_filenames = []
-    flir = CustomFlir()
-    for img_name in Path(paths.path_to_thermal_images).iterdir():
-        flir.process_image(Path(paths.path_to_thermal_images, img_name.name))
-        flir.export_thermal_to_csv(
-            Path(paths.path_to_csv_files, str(img_name.name).split(".")[0] + ".csv")
-        )
-        flir.save_rgb_images(Path(paths.path_to_rgb))
-        list_thermal.append(flir.get_thermal_np())
-        list_filenames.append(str(img_name.name))
-
-    flir.save_normalised_thermal_images(
-        paths.path_to_thermal_images_curated, paths.path_to_csv_files
+
+    CustomFlir(
+        path_to_msx_images=paths.path_to_msx_images,
+        path_to_output_folder=paths.path_to_output_folder,
     )
-    flir.save_temperature_bounds(paths.path_to_txt)
 
 
 if __name__ == "__main__":