Added a pre-commit config file and reformatted all the files accordingly by using it.

toolboxes/Utilities/convert_png2h5.py

@@ -39,7 +39,7 @@ class Cursor(object):
         """
         self.im = im
         self.materials = materials
-        plt.connect('button_press_event', self)
+        plt.connect("button_press_event", self)
 
     def __call__(self, event):
         """
@@ -50,12 +50,19 @@ class Cursor(object):
             x, y = event.xdata, event.ydata
             if x is not None and y is not None:
                 pixel = self.im[int(y), int(x)]
-                pixel = np.floor(pixel * 255).astype(np.int16) # Convert pixel values from float (0-1) to integer (0-255)
+                pixel = np.floor(pixel * 255).astype(
+                    np.int16
+                )  # Convert pixel values from float (0-1) to integer (0-255)
                 match = pixel_match(materials, pixel)
                 if match is False:
-                    logger.info('x, y: {} {} px; RGB: {}; material ID: {}'.format(int(x), int(y), pixel[:-1], len(self.materials)))
+                    logger.info(
+                        "x, y: {} {} px; RGB: {}; material ID: {}".format(
+                            int(x), int(y), pixel[:-1], len(self.materials)
+                        )
+                    )
                     materials.append(pixel)
 
+
 def pixel_match(pixellist, pixeltest):
     """Checks if the RGB(A) value of a pixel already exists in a list of pixel values.
 
@@ -75,31 +82,39 @@ def pixel_match(pixellist, pixeltest):
 
 
 if __name__ == "__main__":
-
     # Parse command line arguments
-    parser = argparse.ArgumentParser(description='Convert a PNG image to a HDF5 file that can be used to import geometry (#geometry_objects_read) into a 2D gprMax model. Colours from the image are selected which correspond to a list of materials that should be supplied in a separate text file.', usage='python convert_png2h5.py imagefile dx dy dz')
-    parser.add_argument('imagefile', help='name of image file including path')
-    parser.add_argument('dxdydz', type=float, action='append', nargs=3, help='spatial resolution of model, e.g. dx dy dz')
-    parser.add_argument('-zcells', default=1, type=int, help='number of cells for domain in z-direction (infinite direction)')
+    parser = argparse.ArgumentParser(
+        description="Convert a PNG image to a HDF5 file that can be used to import geometry (#geometry_objects_read) into a 2D gprMax model. Colours from the image are selected which correspond to a list of materials that should be supplied in a separate text file.",
+        usage="python convert_png2h5.py imagefile dx dy dz",
+    )
+    parser.add_argument("imagefile", help="name of image file including path")
+    parser.add_argument(
+        "dxdydz", type=float, action="append", nargs=3, help="spatial resolution of model, e.g. dx dy dz"
+    )
+    parser.add_argument(
+        "-zcells", default=1, type=int, help="number of cells for domain in z-direction (infinite direction)"
+    )
     args = parser.parse_args()
 
     # Open image file
     im = mpimg.imread(args.imagefile)
 
     # Store image data to use for creating geometry
-    imdata = np.rot90(im, k=3) # Rotate 90CW
-    imdata = np.floor(imdata * 255).astype(np.int16) # Convert pixel values from float (0-1) to integer (0-255)
+    imdata = np.rot90(im, k=3)  # Rotate 90CW
+    imdata = np.floor(imdata * 255).astype(np.int16)  # Convert pixel values from float (0-1) to integer (0-255)
 
-    logger.info('Reading PNG image file: {}'.format(os.path.split(args.imagefile)[1]))
-    logger.info(' 1. Select discrete material colours by clicking on parts of the image.\n 2. When all materials have been selected close the image.')
+    logger.info("Reading PNG image file: {}".format(os.path.split(args.imagefile)[1]))
+    logger.info(
+        " 1. Select discrete material colours by clicking on parts of the image.\n 2. When all materials have been selected close the image."
+    )
 
     # List to hold selected RGB values from image
     materials = []
 
     # Plot image and record rgb values from mouse clicks
-    fig = plt.figure(num=os.path.split(args.imagefile)[1], facecolor='w', edgecolor='w')
-    im = np.flipud(im) # Flip image for viewing with origin in lower left
-    plt.imshow(im, interpolation='nearest', aspect='equal', origin='lower')
+    fig = plt.figure(num=os.path.split(args.imagefile)[1], facecolor="w", edgecolor="w")
+    im = np.flipud(im)  # Flip image for viewing with origin in lower left
+    plt.imshow(im, interpolation="nearest", aspect="equal", origin="lower")
     Cursor(im, materials)
     plt.show()
 
@@ -107,23 +122,22 @@ if __name__ == "__main__":
     dx_dy_dz = (args.dxdydz[0][0], args.dxdydz[0][1], args.dxdydz[0][2])
 
     # Filename for geometry (HDF5) file
-    hdf5file = os.path.splitext(args.imagefile)[0] + '.h5'
+    hdf5file = os.path.splitext(args.imagefile)[0] + ".h5"
 
     # Array to store geometry data (initialised as background, i.e. -1)
     data = np.ones((imdata.shape[0], imdata.shape[1], args.zcells), dtype=np.int16) * -1
 
     # Write geometry (HDF5) file
-    with h5py.File(hdf5file, 'w') as fout:
-
+    with h5py.File(hdf5file, "w") as fout:
         # Add attribute with name 'dx_dy_dz' for spatial resolution
-        fout.attrs['dx_dy_dz'] = dx_dy_dz
+        fout.attrs["dx_dy_dz"] = dx_dy_dz
 
         # Use a boolean mask to match selected pixel values with position in image
         for i, material in enumerate(materials):
             mask = np.all(imdata == material, axis=-1)
-            data[mask,:] = i
+            data[mask, :] = i
 
         # Write data to file
-        fout.create_dataset('data', data=data)
+        fout.create_dataset("data", data=data)
 
-    logger.info('Written HDF5 file: {}'.format(os.path.split(hdf5file)[1]))
+    logger.info("Written HDF5 file: {}".format(os.path.split(hdf5file)[1]))