spacr 0.2.4__py3-none-any.whl → 0.2.8__py3-none-any.whl

spacr/plot.py

@@ -1,4 +1,4 @@
-import os,re, random, cv2, glob, time, math
+import os,re, random, cv2, glob, time, math, torch
 
 import numpy as np
 import pandas as pd
@@ -19,7 +19,113 @@ from IPython.display import Image as ipyimage
 
 from .logger import log_function_call
 
-def plot_masks(batch, masks, flows, cmap='inferno', figuresize=20, nr=1, file_type='.npz', print_object_number=True):
+def plot_image_mask_overlay(file, channels, cell_channel, nucleus_channel, pathogen_channel, figuresize=10, normalize=True, thickness=3, save_pdf=True):
+    """Plot image and mask overlays."""
+
+    def _plot_merged_plot(image, outlines, outline_colors, figuresize, thickness):
+        """Plot the merged plot with overlay, image channels, and masks."""
+
+        def _normalize_image(image, percentiles=(2, 98)):
+            """Normalize the image to the given percentiles."""
+            v_min, v_max = np.percentile(image, percentiles)
+            image_normalized = np.clip((image - v_min) / (v_max - v_min), 0, 1)
+            return image_normalized
+
+        def _generate_contours(mask):
+            """Generate contours for the given mask using OpenCV."""
+            contours, _ = cv2.findContours(mask.astype(np.uint8), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
+            return contours
+
+        def _apply_contours(image, mask, color, thickness):
+            """Apply the contours to the RGB image for each unique label."""
+            unique_labels = np.unique(mask)
+            for label in unique_labels:
+                if label == 0:
+                    continue  # Skip background
+                label_mask = np.where(mask == label, 1, 0).astype(np.uint8)
+                contours = _generate_contours(label_mask)
+                for contour in contours:
+                    cv2.drawContours(image, [contour], -1, mpl.colors.to_rgb(color), thickness)
+            return image
+
+        num_channels = image.shape[-1]
+        fig, ax = plt.subplots(1, num_channels + 1, figsize=(4 * figuresize, figuresize))
+
+        # Plot each channel with its corresponding outlines
+        for v in range(num_channels):
+            channel_image = image[..., v]
+            channel_image_normalized = _normalize_image(channel_image)
+            channel_image_rgb = np.dstack((channel_image_normalized, channel_image_normalized, channel_image_normalized))
+
+            for outline, color in zip(outlines, outline_colors):
+                channel_image_rgb = _apply_contours(channel_image_rgb, outline, color, thickness)
+
+            ax[v].imshow(channel_image_rgb)
+            ax[v].set_title(f'Image - Channel {v}')
+
+        # Plot the combined RGB image with all outlines
+        rgb_image = np.zeros((*image.shape[:2], 3), dtype=float)
+        rgb_channels = min(3, num_channels)
+        for i in range(rgb_channels):
+            channel_image = image[..., i]
+            channel_image_normalized = _normalize_image(channel_image)
+            rgb_image[..., i] = channel_image_normalized
+
+        for outline, color in zip(outlines, outline_colors):
+            rgb_image = _apply_contours(rgb_image, outline, color, thickness)
+
+        ax[-1].imshow(rgb_image)
+        ax[-1].set_title('Combined RGB Image')
+
+        plt.tight_layout()
+
+        # Save the figure as a PDF
+        if save_pdf:
+            pdf_dir = os.path.join(os.path.dirname(os.path.dirname(file)), 'results', 'overlay')
+            os.makedirs(pdf_dir, exist_ok=True)
+            pdf_path = os.path.join(pdf_dir, os.path.basename(file).replace('.npy', '.pdf'))
+            fig.savefig(pdf_path, format='pdf')
+
+        plt.show()
+        return fig
+    
+    stack = np.load(file)
+
+    # Convert to float for normalization and ensure correct handling of both 8-bit and 16-bit arrays
+    if stack.dtype == np.uint16:
+        stack = stack.astype(np.float32)
+    elif stack.dtype == np.uint8:
+        stack = stack.astype(np.float32)
+
+    image = stack[..., channels]
+    outlines = []
+    outline_colors = []
+
+    if pathogen_channel is not None:
+        pathogen_mask_dim = -1  # last dimension
+        outlines.append(np.take(stack, pathogen_mask_dim, axis=2))
+        outline_colors.append('blue')
+
+    if nucleus_channel is not None:
+        nucleus_mask_dim = -2 if pathogen_channel is not None else -1
+        outlines.append(np.take(stack, nucleus_mask_dim, axis=2))
+        outline_colors.append('green')
+
+    if cell_channel is not None:
+        if nucleus_channel is not None and pathogen_channel is not None:
+            cell_mask_dim = -3
+        elif nucleus_channel is not None or pathogen_channel is not None:
+            cell_mask_dim = -2
+        else:
+            cell_mask_dim = -1
+        outlines.append(np.take(stack, cell_mask_dim, axis=2))
+        outline_colors.append('red')
+
+    fig = _plot_merged_plot(image=image, outlines=outlines, outline_colors=outline_colors, figuresize=figuresize, thickness=thickness)
+
+    return
+
+def plot_masks(batch, masks, flows, cmap='inferno', figuresize=10, nr=1, file_type='.npz', print_object_number=True):
     """
     Plot the masks and flows for a given batch of images.
 
@@ -370,7 +476,7 @@ def _filter_objects_in_plot(stack, cell_mask_dim, nucleus_mask_dim, pathogen_mas
 
     return stack
 
-def plot_arrays(src, figuresize=50, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
+def plot_arrays(src, figuresize=10, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
     """
     Plot randomly selected arrays from a given directory.
 
@@ -764,7 +870,7 @@ def _save_scimg_plot(src, nr_imgs=16, channel_indices=[0,1,2], um_per_pixel=0.1,
 
     return
 
-def _plot_cropped_arrays(stack, filename, figuresize=20, cmap='inferno', threshold=500):
+def _plot_cropped_arrays(stack, filename, figuresize=10, cmap='inferno', threshold=500):
     """
     Plot cropped arrays.
 
@@ -802,49 +908,9 @@ def _plot_cropped_arrays(stack, filename, figuresize=20, cmap='inferno', thresho
         fig, axs = plt.subplots(1, num_channels, figsize=(figuresize, figuresize))
         for channel in range(num_channels):
             plot_single_array(stack[:, :, channel], axs[channel], f'C. {channel}', plt.get_cmap(cmap))
-        fig.tight_layout()
-        plt.show()
-    
-    #stop = time.time()
-    #duration = stop - start
-    #print('plot_cropped_arrays', duration)
+        fig.tight_layout()    
     print(f'{filename}')
-
-def _plot_cropped_arrays_v1(stack, figuresize=20, cmap='inferno'):
-    """
-    Plot cropped arrays.
-
-    Args:
-        stack (ndarray): The array to be plotted.
-        figuresize (int, optional): The size of the figure. Defaults to 20.
-        cmap (str, optional): The colormap to be used. Defaults to 'inferno'.
-
-    Returns:
-        None
-    """
-    start = time.time()
-    dim = stack.shape 
-    channel=min(dim)
-    if len(stack.shape) == 2:
-        f, a = plt.subplots(1, 1,figsize=(figuresize,figuresize))
-        a.imshow(stack, cmap=plt.get_cmap(cmap))
-        a.set_title('Channel one',size=18)
-        a.axis('off')
-        f.tight_layout()
-        plt.show()
-    if len(stack.shape) > 2:
-        anr = stack.shape[2]
-        f, a = plt.subplots(1, anr,figsize=(figuresize,figuresize))
-        for channel in range(anr):
-            a[channel].imshow(stack[:,:,channel], cmap=plt.get_cmap(cmap))
-            a[channel].set_title('Channel '+str(channel),size=18)
-            a[channel].axis('off')
-            f.tight_layout()
-        plt.show()
-    stop = time.time()
-    duration = stop - start
-    print('plot_cropped_arrays', duration)
-    return
+    return fig
     
 def _visualize_and_save_timelapse_stack_with_tracks(masks, tracks_df, save, src, name, plot, filenames, object_type, mode='btrack', interactive=False):
     """
@@ -931,7 +997,7 @@ def _display_gif(path):
     with open(path, 'rb') as file:
         display(ipyimage(file.read()))
         
-def _plot_recruitment(df, df_type, channel_of_interest, target, columns=[], figuresize=50):
+def _plot_recruitment(df, df_type, channel_of_interest, target, columns=[], figuresize=10):
     """
     Plot recruitment data for different conditions and pathogens.
 
@@ -1120,6 +1186,52 @@ def _imshow(img, labels, nrow=20, color='white', fontsize=12):
         y = row * img_height + 15
         plt.text(x, y, label, color=color, fontsize=fontsize, fontweight='bold')
     return fig
+
+def _imshow_gpu(img, labels, nrow=20, color='white', fontsize=12):
+    """
+    Display multiple images in a grid with corresponding labels.
+
+    Args:
+        img (torch.Tensor): A batch of images as a tensor.
+        labels (list): List of labels corresponding to each image.
+        nrow (int, optional): Number of images per row in the grid. Defaults to 20.
+        color (str, optional): Color of the label text. Defaults to 'white'.
+        fontsize (int, optional): Font size of the label text. Defaults to 12.
+    """
+    if img.is_cuda:
+        img = img.cpu()  # Move to CPU if the tensor is on GPU
+
+    n_images = len(labels)
+    n_col = nrow
+    n_row = int(np.ceil(n_images / n_col))
+
+    img_height = img.shape[2]  # Height of the image
+    img_width = img.shape[3]   # Width of the image
+
+    # Prepare the canvas on CPU
+    canvas = torch.zeros((img_height * n_row, img_width * n_col, 3))
+
+    for i in range(n_row):
+        for j in range(n_col):
+            idx = i * n_col + j
+            if idx < n_images:
+                # Place the image on the canvas
+                canvas[i * img_height:(i + 1) * img_height, j * img_width:(j + 1) * img_width] = img[idx].permute(1, 2, 0)
+
+    canvas = canvas.numpy()  # Convert to NumPy for plotting
+
+    fig = plt.figure(figsize=(50, 50))
+    plt.imshow(canvas)
+    plt.axis("off")
+
+    for i, label in enumerate(labels):
+        row = i // n_col
+        col = i % n_col
+        x = col * img_width + 2
+        y = row * img_height + 15
+        plt.text(x, y, label, color=color, fontsize=fontsize, fontweight='bold')
+
+    return fig
     
 def _plot_histograms_and_stats(df):
     conditions = df['condition'].unique()

spacr/resources/font/open_sans/OFL.txt

@@ -0,0 +1,93 @@
+Copyright 2020 The Open Sans Project Authors (https://github.com/googlefonts/opensans)
+
+This Font Software is licensed under the SIL Open Font License, Version 1.1.
+This license is copied below, and is also available with a FAQ at:
+https://openfontlicense.org
+
+
+-----------------------------------------------------------
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+-----------------------------------------------------------
+
+PREAMBLE
+The goals of the Open Font License (OFL) are to stimulate worldwide
+development of collaborative font projects, to support the font creation
+efforts of academic and linguistic communities, and to provide a free and
+open framework in which fonts may be shared and improved in partnership
+with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves. The
+fonts, including any derivative works, can be bundled, embedded, 
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works. The fonts and derivatives,
+however, cannot be released under any other type of license. The
+requirement for fonts to remain under this license does not apply
+to any document created using the fonts or their derivatives.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components as
+distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to a
+new environment.
+
+"Author" refers to any designer, engineer, programmer, technical
+writer or other person who contributed to the Font Software.
+
+PERMISSION & CONDITIONS
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,
+in Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+redistributed and/or sold with any software, provided that each copy
+contains the above copyright notice and this license. These can be
+included either as stand-alone text files, human-readable headers or
+in the appropriate machine-readable metadata fields within text or
+binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+Name(s) unless explicit written permission is granted by the corresponding
+Copyright Holder. This restriction only applies to the primary font name as
+presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+Software shall not be used to promote, endorse or advertise any
+Modified Version, except to acknowledge the contribution(s) of the
+Copyright Holder(s) and the Author(s) or with their explicit written
+permission.
+
+5) The Font Software, modified or unmodified, in part or in whole,
+must be distributed entirely under this license, and must not be
+distributed under any other license. The requirement for fonts to
+remain under this license does not apply to any document created
+using the Font Software.
+
+TERMINATION
+This license becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+OTHER DEALINGS IN THE FONT SOFTWARE.

spacr/resources/font/open_sans/README.txt

@@ -0,0 +1,100 @@
+Open Sans Variable Font
+=======================
+
+This download contains Open Sans as both variable fonts and static fonts.
+
+Open Sans is a variable font with these axes:
+  wdth
+  wght
+
+This means all the styles are contained in these files:
+  OpenSans-VariableFont_wdth,wght.ttf
+  OpenSans-Italic-VariableFont_wdth,wght.ttf
+
+If your app fully supports variable fonts, you can now pick intermediate styles
+that aren’t available as static fonts. Not all apps support variable fonts, and
+in those cases you can use the static font files for Open Sans:
+  static/OpenSans_Condensed-Light.ttf
+  static/OpenSans_Condensed-Regular.ttf
+  static/OpenSans_Condensed-Medium.ttf
+  static/OpenSans_Condensed-SemiBold.ttf
+  static/OpenSans_Condensed-Bold.ttf
+  static/OpenSans_Condensed-ExtraBold.ttf
+  static/OpenSans_SemiCondensed-Light.ttf
+  static/OpenSans_SemiCondensed-Regular.ttf
+  static/OpenSans_SemiCondensed-Medium.ttf
+  static/OpenSans_SemiCondensed-SemiBold.ttf
+  static/OpenSans_SemiCondensed-Bold.ttf
+  static/OpenSans_SemiCondensed-ExtraBold.ttf
+  static/OpenSans-Light.ttf
+  static/OpenSans-Regular.ttf
+  static/OpenSans-Medium.ttf
+  static/OpenSans-SemiBold.ttf
+  static/OpenSans-Bold.ttf
+  static/OpenSans-ExtraBold.ttf
+  static/OpenSans_Condensed-LightItalic.ttf
+  static/OpenSans_Condensed-Italic.ttf
+  static/OpenSans_Condensed-MediumItalic.ttf
+  static/OpenSans_Condensed-SemiBoldItalic.ttf
+  static/OpenSans_Condensed-BoldItalic.ttf
+  static/OpenSans_Condensed-ExtraBoldItalic.ttf
+  static/OpenSans_SemiCondensed-LightItalic.ttf
+  static/OpenSans_SemiCondensed-Italic.ttf
+  static/OpenSans_SemiCondensed-MediumItalic.ttf
+  static/OpenSans_SemiCondensed-SemiBoldItalic.ttf
+  static/OpenSans_SemiCondensed-BoldItalic.ttf
+  static/OpenSans_SemiCondensed-ExtraBoldItalic.ttf
+  static/OpenSans-LightItalic.ttf
+  static/OpenSans-Italic.ttf
+  static/OpenSans-MediumItalic.ttf
+  static/OpenSans-SemiBoldItalic.ttf
+  static/OpenSans-BoldItalic.ttf
+  static/OpenSans-ExtraBoldItalic.ttf
+
+Get started
+-----------
+
+1. Install the font files you want to use
+
+2. Use your app's font picker to view the font family and all the
+available styles
+
+Learn more about variable fonts
+-------------------------------
+
+  https://developers.google.com/web/fundamentals/design-and-ux/typography/variable-fonts
+  https://variablefonts.typenetwork.com
+  https://medium.com/variable-fonts
+
+In desktop apps
+
+  https://theblog.adobe.com/can-variable-fonts-illustrator-cc
+  https://helpx.adobe.com/nz/photoshop/using/fonts.html#variable_fonts
+
+Online
+
+  https://developers.google.com/fonts/docs/getting_started
+  https://developer.mozilla.org/en-US/docs/Web/CSS/CSS_Fonts/Variable_Fonts_Guide
+  https://developer.microsoft.com/en-us/microsoft-edge/testdrive/demos/variable-fonts
+
+Installing fonts
+
+  MacOS: https://support.apple.com/en-us/HT201749
+  Linux: https://www.google.com/search?q=how+to+install+a+font+on+gnu%2Blinux
+  Windows: https://support.microsoft.com/en-us/help/314960/how-to-install-or-remove-a-font-in-windows
+
+Android Apps
+
+  https://developers.google.com/fonts/docs/android
+  https://developer.android.com/guide/topics/ui/look-and-feel/downloadable-fonts
+
+License
+-------
+Please read the full license text (OFL.txt) to understand the permissions,
+restrictions and requirements for usage, redistribution, and modification.
+
+You can use them in your products & projects – print or digital,
+commercial or otherwise.
+
+This isn't legal advice, please consider consulting a lawyer and see the full
+license for all details.