feat: physical scale bar length

README.md

@@ -103,6 +103,8 @@ show_box_background=True,
 
 ```show_box_background (bool)```: Add black background with 50% transparency to the name and scalebar box. *Default: True*
 
+```in_physical_units (bool)```: If True, scale_length is interpreted as physical length in the same units as pixel_size. If False, scale_length is a fraction of image width. *Default: False*
+
 
 ### 2. Process Image
 Pass a single image or a list of images to be processed:

lutipy/core.py

@@ -9,15 +9,17 @@ class LUTiPy:
     """Main interface for processing and visualizing images using LUTs."""
 
     def __init__(self, rgb: tuple = (255, 0, 255), channel_names: list = None, layout: str = 'grid', scale_length: float = 0.25, pixel_size: str = None, name_position="top-left", show_box_background=True,
-                 scalebar=False, scalebar_position="bottom-left"):
+                 scalebar=False, scalebar_position="bottom-left", in_physical_units=False):
         """Initialize the LUTIPy object.
 
         Args:
             rgb (tuple): Base RGB color for LUT generation.
             channel_names (list): Names for each channel in the image.
             layout (str): Layout for the panel ('grid' or 'horizontal').
-            scale_length (float): Scale bar length as a fraction of image width.
+            scale_length (float): Scale bar length. If in_physical_units is False, this is a fraction of image width.
+                                If in_physical_units is True, this is the physical length in the same units as pixel_size.
             pixel_size (str): Physical size of a pixel (e.g., "10 nm").
+            in_physical_units (bool): If True, scale_length is interpreted as physical length. If False, it's a fraction of image width.
         """
         self.rgb = rgb
         self.channel_names = channel_names
@@ -28,20 +30,22 @@ def __init__(self, rgb: tuple = (255, 0, 255), channel_names: list = None, layou
         self.show_box_background = show_box_background
         self.scalebar = scalebar
         self.scalebar_position = scalebar_position
+        self.in_physical_units = in_physical_units
 
     def _convert_pixel_size(self, image: np.ndarray, pixel_size: str) -> float:
         """Convert pixel size to a float value in meters."""
         try:
             value, unit = pixel_size.split()
             value = float(value)
             unit = unit.lower()
-
         except ValueError as e:
             raise ValueError(f"Invalid pixel size format: {pixel_size}") from e
 
-        value = float(value)*image.shape[1]
-
-        return f"{value} {unit}"
+        if not self.in_physical_units:
+            # For fraction case, multiply by image width to get total width
+            value = float(value) * image.shape[1]
+
+        return value
 
 
 
@@ -54,16 +58,13 @@ def process_image(self, image: np.ndarray) -> None:
         Returns:
             None
         """
-
-        """
-        TODO:
-        1. Check the scale and modify wrt image resizing, otherwise it is incorrect.
-        """
         image = ImageProcessor.convert_to_channel_last(image)
         image_8bit = ImageProcessor.convert_to_8bit(image)
-        pixel_size = self._convert_pixel_size(image_8bit, self.pixel_size)
+        pixel_size_value = self._convert_pixel_size(image_8bit, self.pixel_size)
         aspect_ratio = image_8bit.shape[1] / image_8bit.shape[0]
+        original_width = image_8bit.shape[1]
         image_8bit = ImageProcessor.resize_image(image_8bit, (400,int(400*aspect_ratio)))
+        resize_factor = image_8bit.shape[1] / original_width
         num_channels = image_8bit.shape[-1]
         complementary_colors = ComplementaryColors(self.rgb).find_n_complementary_colors(num_channels)
         composite_image = ImageProcessor.apply_complementary_luts(image_8bit, complementary_colors)
@@ -75,10 +76,12 @@ def process_image(self, image: np.ndarray) -> None:
         self._figure = PanelCreator.create_panel(
             image_8bit, complementary_colors, self.channel_names,
             ImageProcessor.apply_complementary_luts(image_8bit, complementary_colors),
-            layout=self.layout, scale_length=self.scale_length, pixel_size=pixel_size, 
-            name_position = self.name_position,
-            show_box_background = self.show_box_background,
-            scalebar=self.scalebar, scalebar_position=self.scalebar_position
+            layout=self.layout, scale_length=self.scale_length, pixel_size=self.pixel_size, 
+            name_position=self.name_position,
+            show_box_background=self.show_box_background,
+            scalebar=self.scalebar, scalebar_position=self.scalebar_position,
+            in_physical_units=self.in_physical_units,
+            resize_factor=resize_factor
         )
 
     def save_figure(self, filename: str) -> None:

lutipy/utils.py

@@ -496,12 +496,14 @@ def create_panel(
         channel_names: list,
         composite_image: np.ndarray,
         scale_length: float = 0.25,
-        pixel_size: float = None,  # Pixel size in physical units, required for scalebar
+        pixel_size: str = None,  # Pixel size in physical units, required for scalebar
         layout: str = 'grid',
         name_position: str = 'bottom-center',
         show_box_background: bool = True,
         scalebar: bool = False,  # Whether to add a scalebar
-        scalebar_position: str = 'bottom-right'  # Position of the scalebar
+        scalebar_position: str = 'bottom-right',  # Position of the scalebar
+        in_physical_units: bool = False,  # Whether scale_length is in physical units
+        resize_factor: float = 1.0  # Factor by which the image was resized
     ) -> plt.Figure:
         """
         Create a tiled panel image with user-defined name positioning and optional scalebar.
@@ -511,13 +513,15 @@ def create_panel(
             luts (list): List of LUT colors (RGB tuples).
             channel_names (list): Names for each channel.
             composite_image (np.ndarray): Composite RGB image.
-            scale_length (float): Length of the scalebar as a fraction of the image width.
-            pixel_size (float): Physical size of a pixel (e.g., 0.1 micrometers). Required if scalebar is True.
+            scale_length (float): Length of the scalebar. If in_physical_units is False, this is a fraction of image width.
+                                If in_physical_units is True, this is the physical length in the same units as pixel_size.
+            pixel_size (str): Physical size of a pixel (e.g., "0.31 nm"). Required if scalebar is True.
             layout (str): Layout of the panel ('grid', 'horizontal', 'vertical').
             name_position (str): Position of channel names ('bottom-center', 'top-left', etc.).
             show_box_background (bool): Whether to show a black background behind names.
             scalebar (bool): Whether to add a scalebar.
             scalebar_position (str): Position of the scalebar ('bottom-right', 'top-left', etc.).
+            in_physical_units (bool): If True, scale_length is interpreted as physical length. If False, it's a fraction of image width.
 
         Returns:
             plt.Figure: The figure object for the created panel.
@@ -553,7 +557,7 @@ def create_panel(
         if scalebar:
             if pixel_size is None:
                 raise ValueError("Pixel size must be provided for scalebar.")
-            PanelCreator._add_scalebar(axes[num_channels], scale_length, pixel_size, scalebar_text_position, image.shape, show_box_background)
+            PanelCreator._add_scalebar(axes[num_channels], scale_length, pixel_size, scalebar_text_position, image.shape, show_box_background, in_physical_units, resize_factor)
 
         # Hide any unused axes
         for j in range(num_channels + 1, len(axes)):
@@ -625,10 +629,23 @@ def _display_channel(axis, channel: np.ndarray, lut: tuple, name: str, text_posi
         )
 
     @staticmethod
-    def _add_scalebar(axis, scale_length: float, pixel_size: float, text_position: dict, image_shape: tuple, show_box_background: bool):
+    def _add_scalebar(axis, scale_length: float, pixel_size: str, text_position: dict, image_shape: tuple, show_box_background: bool, in_physical_units: bool = False, resize_factor: float = 1.0):
         """Add a scalebar to the image."""
-        scale_bar_length_px = int(image_shape[1] * scale_length)
-        scale_bar_length_physical = scale_length * float(pixel_size.split(" ")[0])  # Physical length
+        # Calculate scale bar length in pixels
+        if in_physical_units:
+            # Convert physical length to pixels, accounting for image resize to 400x400
+            pixel_size_value = float(pixel_size.split(" ")[0])
+            scale_bar_length_px = int((scale_length / pixel_size_value) * resize_factor)
+            scale_bar_length_physical = scale_length
+        else:
+            # Use fraction of image width
+            scale_bar_length_px = int(image_shape[1] * scale_length)
+            # For fraction case, calculate physical length from pixel size and total width
+            # IMportant note: image_shape is already the resized image shape
+            pixel_size_value = float(pixel_size.split(" ")[0])
+            # total width in physical units for the resized image
+            total_width = (image_shape[1] / resize_factor) * pixel_size_value
+            scale_bar_length_physical = total_width * scale_length
 
         # Calculate dynamic starting positions based on text_position
         x_start = text_position['x'] - (scale_bar_length_px / (2 * image_shape[1])) if text_position['ha'] == 'center' else (
@@ -652,7 +669,6 @@ def _add_scalebar(axis, scale_length: float, pixel_size: float, text_position: d
                 )
             )
 
-
         axis.plot(
             [x_start, x_end], [y_start, y_start], color='white', lw=3,
             transform=axis.transAxes, clip_on=False

requirements.txt

@@ -1,2 +1,3 @@
 numpy
-matplotlib
+matplotlib
+imageio