From f5516fa177ac8a131c20cfc7931f541dc6bc7d12 Mon Sep 17 00:00:00 2001
From: fima <fima@dtu.dk>
Date: Mon, 4 Mar 2024 14:32:51 +0100
Subject: [PATCH] Annotation tool 4 0
---
docs/notebooks/annotation_tool.ipynb | 120 +------
docs/utils.md | 5 +
qim3d/css/gradio.css | 131 ++++++--
qim3d/gui/annotation_tool.py | 467 +++++++++++----------------
qim3d/utils/__init__.py | 3 +-
qim3d/utils/img.py | 46 +++
6 files changed, 354 insertions(+), 418 deletions(-)
create mode 100644 qim3d/utils/img.py
diff --git a/docs/notebooks/annotation_tool.ipynb b/docs/notebooks/annotation_tool.ipynb
index 066b0766..9089f962 100644
--- a/docs/notebooks/annotation_tool.ipynb
+++ b/docs/notebooks/annotation_tool.ipynb
@@ -1,13 +1,5 @@
{
"cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Image annotation tool\n",
- "This notebook shows how the annotation interface can be used to create masks for images"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -15,113 +7,19 @@
"outputs": [],
"source": [
"import qim3d\n",
+ "from scipy import ndimage\n",
"import matplotlib.pyplot as plt\n",
- "import matplotlib as mpl\n",
- "import numpy as np\n",
- "%matplotlib inline"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Load 2D example image\n",
- "img = qim3d.examples.blobs_256x256\n",
+ "qim3d.io.logger.level(\"info\")\n",
+ "\n",
+ "# Load example image\n",
+ "img = qim3d.examples.bone_128x128x128\n",
"\n",
- "# Display image\n",
- "plt.imshow(img)\n",
- "plt.show()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
"# Start annotation tool\n",
"interface = qim3d.gui.annotation_tool.Interface()\n",
- "interface.max_masks = 4\n",
"\n",
"# We can directly pass the image we loaded to the interface\n",
- "interface.launch(img=img)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# When 'prepare mask for download' is pressed once, the mask can be retrieved with the get_result() method\n",
- "mask = interface.get_result()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Check the obtained mask"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "print (f\"Original image shape..: {img.shape}\")\n",
- "print (f\"Mask image shape......: {mask.shape}\")\n",
- "print (f\"\\nNumber of masks: {np.max(mask)}\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Show the masked regions"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "%matplotlib inline\n",
- "\n",
- "nmasks = np.max(mask)\n",
- "fig, axs = plt.subplots(nrows=1, ncols=nmasks+2, figsize=(12,3))\n",
- "\n",
- "# Show original image\n",
- "axs[0].imshow(img)\n",
- "axs[0].set_title(\"Original\")\n",
- "axs[0].axis('off')\n",
- "\n",
- "\n",
- "# Show masks\n",
- "cmap = mpl.colormaps[\"rainbow\"].copy()\n",
- "cmap.set_under(color='black') # Sets the background to black\n",
- "axs[1].imshow(mask, interpolation='none', cmap=cmap, vmin=1, vmax=nmasks+1)\n",
- "axs[1].set_title(\"Masks\")\n",
- "axs[1].axis('off')\n",
- "\n",
- "# Show masked regions\n",
- "for idx in np.arange(2, nmasks+2):\n",
- " mask_id = idx-1\n",
- " submask = mask.copy()\n",
- " submask[submask != mask_id] = 0\n",
- " \n",
- " masked_img = img.copy()\n",
- " masked_img[submask==0] = 0\n",
- " axs[idx].imshow(masked_img)\n",
- " axs[idx].set_title(f\"Mask {mask_id}\")\n",
- "\n",
- " axs[idx].axis('off')\n",
- "\n",
- "plt.show()"
+ "#interface.launch()\n",
+ "interface.launch(ndimage.zoom(img[0], 3, order=0))"
]
}
],
@@ -141,9 +39,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.11"
+ "version": "3.11.5"
}
},
"nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
}
diff --git a/docs/utils.md b/docs/utils.md
index d35d6ca3..3d4d38ec 100644
--- a/docs/utils.md
+++ b/docs/utils.md
@@ -6,6 +6,11 @@ icon: fontawesome/solid/screwdriver-wrench
A set of tools to ease managment of the system, with the common needs for large data in mind.
+::: qim3d.utils.img
+ options:
+ members:
+ - overlay_rgb_images
+
::: qim3d.utils.system
options:
members:
diff --git a/qim3d/css/gradio.css b/qim3d/css/gradio.css
index 6e01ef35..9039d6d6 100644
--- a/qim3d/css/gradio.css
+++ b/qim3d/css/gradio.css
@@ -1,5 +1,5 @@
/* Override for dark mode */
-.dark{
+.dark {
--name: default;
--primary-50: #fff7ed;
--primary-100: #ffedd5;
@@ -73,9 +73,9 @@
--link-text-color-hover: var(--secondary-700);
--link-text-color-visited: var(--secondary-500);
--body-text-color-subdued: var(--neutral-400);
- --shadow-drop: rgba(0,0,0,0.05) 0px 1px 2px 0px;
+ --shadow-drop: rgba(0, 0, 0, 0.05) 0px 1px 2px 0px;
--shadow-drop-lg: 0 1px 3px 0 rgb(0 0 0 / 0.1), 0 1px 2px -1px rgb(0 0 0 / 0.1);
- --shadow-inset: rgba(0,0,0,0.05) 0px 2px 4px 0px inset;
+ --shadow-inset: rgba(0, 0, 0, 0.05) 0px 2px 4px 0px inset;
--shadow-spread: 3px;
--block-background-fill: var(--background-fill-primary);
--block-border-color: var(--border-color-primary);
@@ -203,6 +203,7 @@
--button-small-text-weight: 400;
--button-transition: none;
}
+
/* Up here is the override for dark mode */
/* Now comes our custom CSS */
@@ -228,9 +229,10 @@ h2 {
white-space: pre !important;
}
-.no-border{
+.no-border {
border-width: 0px !important;
}
+
/* Hides Gradio footer */
footer {
visibility: hidden;
@@ -341,9 +343,9 @@ input[type="range"]::-webkit-slider-thumb {
}
/* Buttons */
-.btn-html{
+.btn-html {
position: sticky;
- display:flex;
+ display: flex;
justify-content: center;
background: white !important;
border-color: #6c757d !important;
@@ -372,7 +374,7 @@ input[type="range"]::-webkit-slider-thumb {
text-align: left !important;
}
-.btn-spinner::after{
+.btn-spinner::after {
content: "";
position: absolute;
width: 16px;
@@ -547,7 +549,7 @@ div.svelte-1frtwj3 {
.w-64 {
width: 64px !important;
- min-width: 64px !important;
+ min-width: 64px !important;
}
@@ -558,7 +560,7 @@ div.svelte-1frtwj3 {
.w-36 {
width: 36px !important;
- min-width: 36px !important;
+ min-width: 36px !important;
}
@@ -569,7 +571,7 @@ div.svelte-1frtwj3 {
.w-32 {
width: 32px !important;
- min-width: 32px !important;
+ min-width: 32px !important;
}
@@ -579,7 +581,7 @@ div.svelte-1frtwj3 {
.w-16 {
width: 16px !important;
- min-width: 16px !important;
+ min-width: 16px !important;
}
.h-0 {
@@ -590,33 +592,124 @@ div.svelte-1frtwj3 {
width: 0px !important;
}
-.options{
+.options {
border: 1px solid #bababa !important;
box-shadow: 0px 0px 8px rgba(0, 0, 0, 0.15) !important;
}
-.mt-32{
+.mt-32 {
margin-top: 32px;
}
-.mt-48{
+.mt-48 {
margin-top: 48px;
}
-.mt-64{
+.mt-64 {
margin-top: 64px;
}
-.mt-128{
+.mt-128 {
margin-top: 128px;
}
-.hide-overflow{
+.hide-overflow {
overflow: hidden !important;
}
-.wrap.default{
+.wrap.default {
visibility: hidden !important;
-}
\ No newline at end of file
+}
+
+
+/* Annotation tool CSS */
+
+.annotation-tool .layer-wrap {
+ display: none !important;
+}
+
+.annotation-tool button[title="Image button"] {
+ display: none !important;
+}
+
+.annotation-tool:not(.no-img) button[title="Upload button"] {
+ display: none !important;
+}
+
+.annotation-tool button[title="Clear canvas"] {
+ display: none !important;
+}
+
+.annotation-tool button[title="Color button"] {
+ color: var(--block-label-text-color) !important;
+ margin-inline-end: 32px !important;
+}
+
+.annotation-tool button[title="Color button"]::after {
+ content: "Select mask";
+}
+
+.annotation-tool button[title="Size button"] {
+ color: var(--block-label-text-color) !important;
+}
+
+
+.annotation-tool button[title="Size button"]::after {
+ content: "Brush size";
+}
+
+
+.annotation-tool .row-wrap {
+ justify-content: flex-start !important;
+}
+
+.annotation-tool .controls-wrap .small {
+ width: 20px !important;
+ height: 20px !important;
+}
+
+.annotation-tool .controls-wrap {
+ top: 0px !important;
+ left: 0px !important;
+}
+
+.annotation-tool .controls-wrap .padded {
+ padding: 8px !important;
+ border: 0px !important;
+ background-color: rgba(255, 255, 255, 0.8);
+}
+
+.annotation-tool .stage-wrap {
+ margin-top: 0px !important;
+ margin-bottom: 16px !important;
+}
+
+.annotation-tool .svelte-b3dw9m {
+ display: flex !important;
+ visibility: visible !important;
+ opacity: 1 !important;
+}
+
+.annotation-tool .bottom {
+ bottom: 8px !important;
+ left: 0px !important;
+ position: absolute !important;
+}
+
+.annotation-tool .download {
+ min-width: 4rem !important;
+ width: 10%;
+ white-space: nowrap;
+ text-align: right;
+}
+
+.annotation-tool .stage-wrap canvas {
+ border: 0px !important;
+ max-width: 512px !important;
+ max-height: 512px !important;
+ height: 512px !important;
+ width: fit-content !important;
+
+}
diff --git a/qim3d/gui/annotation_tool.py b/qim3d/gui/annotation_tool.py
index 230ad9cb..d6209d40 100644
--- a/qim3d/gui/annotation_tool.py
+++ b/qim3d/gui/annotation_tool.py
@@ -1,21 +1,32 @@
import tifffile
import os
+import time
+import getpass
import numpy as np
import gradio as gr
-from qim3d.io import load # load or DataLoader?
-from qim3d.utils import internal_tools
+import qim3d.utils
+from qim3d.io import load, save
+from qim3d.io.logger import log
+
+
+class Session:
+ def __init__(self):
+ self.n_masks = 3
+ self.img_editor = None
+ self.masks_rgb = None
+ self.mask_names = {0: "red", 1: "green", 2: "blue"}
+ self.temp_files = []
+ self.gradio_temp = None
+ self.username = getpass.getuser()
class Interface:
def __init__(self):
self.verbose = False
self.title = "Annotation tool"
- # self.plot_height = 768
- self.height = 1024
- # self.width = 960
- self.max_masks = 3
- self.mask_opacity = 0.5
- self.cmy_hex = ["#00ffff", "#ff00ff", "#ffff00"] # Colors for max_masks>3?
+ self.height = 768
+ self.interface = None
+ self.username = getpass.getuser()
# CSS path
current_dir = os.path.dirname(os.path.abspath(__file__))
@@ -23,7 +34,9 @@ class Interface:
def launch(self, img=None, **kwargs):
# Create gradio interfaces
- self.interface = self.create_interface(img=img)
+
+ self.interface = self.create_interface(img)
+ self.gradio_temp = self.interface.GRADIO_CACHE
# Set gradio verbose level
if self.verbose:
@@ -35,7 +48,6 @@ class Interface:
quiet=quiet,
height=self.height,
# width=self.width,
- show_tips=False,
**kwargs,
)
@@ -43,322 +55,203 @@ class Interface:
def get_result(self):
# Get the temporary files from gradio
- temp_sets = self.interface.temp_file_sets
- for temp_set in temp_sets:
- if "mask" in str(temp_set):
+ base = os.path.join(self.gradio_temp, "qim3d", self.username)
+ temp_path_list = []
+ for filename in os.listdir(base):
+ if "mask" in str(filename):
# Get the list of the temporary files
- temp_path_list = list(temp_set)
-
- # Files are not in creation order,
- # so we need to get find the latest
- creation_time_list = []
- for path in temp_path_list:
- creation_time_list.append(os.path.getctime(path))
+ temp_path_list.append(os.path.join(base, filename))
- # Get index for the latest file
- file_idx = np.argmax(creation_time_list)
+ # Make dictionary of maks
+ masks = {}
+ for temp_file in temp_path_list:
+ mask_file = os.path.basename(temp_file)
+ mask_name = os.path.splitext(mask_file)[0]
+ masks[mask_name] = load(temp_file)
- # Load the temporary file
- mask = load(temp_path_list[file_idx])
+ return masks
- return mask
+ def set_visible(self):
+ return gr.update(visible=True)
def create_interface(self, img=None):
+
+ if img is not None:
+ custom_css = "annotation-tool"
+ else:
+ custom_css = "annotation-tool no-img"
+
with gr.Blocks(css=self.css_path) as gradio_interface:
- masks_state = gr.State(value={})
- counts = gr.Number(value=1, visible=False)
+ brush = gr.Brush(
+ colors=[
+ "rgb(255,50,100)",
+ "rgb(50,250,100)",
+ "rgb(50,100,255)",
+ ],
+ color_mode="fixed",
+ default_size=10,
+ )
with gr.Row():
- with gr.Column(scale=1, min_width=320):
- upload_img_btn = gr.UploadButton(
- label="Upload image",
- file_types=["image"],
- interactive=True if img is None else False,
- )
- clear_img_btn = gr.Button(
- value="Clear image", interactive=False if img is None else True
+
+ with gr.Column(scale=6):
+ img_editor = gr.ImageEditor(
+ value=img,
+ type="numpy",
+ image_mode="RGB",
+ brush=brush,
+ sources="upload",
+ interactive=True,
+ show_download_button=True,
+ container=False,
+ transforms=[""],
+ elem_classes=custom_css,
)
+ with gr.Column(scale=1, min_width=256):
+
with gr.Row():
- with gr.Column(scale=2, min_width=32):
- selected_mask = gr.Radio(
- choices=["Mask 1"],
- value="Mask 1",
- label="Choose which mask to draw",
- scale=1,
- )
- with gr.Column(scale=1, min_width=64):
- add_mask_btn = gr.Button(
- value="Add mask",
- scale=2,
- )
+ btn_update = gr.Button(
+ value="Update", elem_classes="btn btn-html btn-run"
+ )
+
with gr.Row():
- prep_dl_btn = gr.Button(
- value="Prepare mask for download",
- visible=False if img is None else True,
+ overlay_img = gr.Image(
+ show_download_button=False, show_label=False, visible=False
)
with gr.Row():
- save_output = gr.File(
- show_label=True,
- label="Output file",
+ masks_download = gr.File(
+ label="Download masks",
visible=False,
+ elem_classes=custom_css,
)
- with gr.Column(scale=4):
- with gr.Row():
- input_img = gr.Image(
- label="Input",
- tool="sketch",
- value=img,
- height=600,
- width=600,
- brush_color="#00ffff",
- mask_opacity=self.mask_opacity,
- interactive=False if img is None else True,
- )
+ temp_path = gr.Textbox(value=gradio_interface.GRADIO_CACHE, visible=False)
+ session = gr.State([])
+ inputs = [img_editor]
+ operations = Operations()
+ # fmt: off
+ btn_update.click(
+ fn=operations.start_session, inputs=[img_editor,temp_path] , outputs=session).then(
+ fn=operations.preview, inputs=session, outputs=overlay_img).then(
+ fn=self.set_visible, inputs=None, outputs=overlay_img).then(
+ fn=operations.separate_masks, inputs=session, outputs=[session, masks_download]).then(
+ fn=self.set_visible, inputs=None, outputs=masks_download)
+
+ # fmt: on
+ return gradio_interface
- output_masks = []
- for mask_idx in range(self.max_masks):
- with gr.Row(): # make a new row for every mask
- output_mask = gr.Image(
- label=f"Mask {mask_idx+1}",
- visible=True if mask_idx == 0 else False,
- image_mode="L",
- height=600,
- width=600,
- interactive=False
- if img is None
- else True, # If statement added bc of bug after Gradio 3.44.x
- show_download_button=False,
- )
- output_masks.append(output_mask)
-
- # Operations
- operations = Operations(max_masks=self.max_masks, cmy_hex=self.cmy_hex)
-
- # Update component configuration when image is uploaded
- upload_img_btn.upload(
- fn=operations.upload_img_update,
- inputs=upload_img_btn,
- outputs=[input_img, clear_img_btn, upload_img_btn, prep_dl_btn]
- + output_masks,
- )
- # Add mask below when 'add mask' button is clicked
- add_mask_btn.click(
- fn=operations.increment_mask,
- inputs=counts,
- outputs=[counts, selected_mask] + output_masks,
- )
+class Operations:
- # Draw mask when input image is edited
- input_img.edit(
- fn=operations.update_masks,
- inputs=[input_img, selected_mask, masks_state, upload_img_btn],
- outputs=output_masks,
- )
+ def start_session(self, *args):
+ session = Session()
+ session.img_editor = args[0]
+ session.gradio_temp = args[1]
- # Update brush color according to radio setting
- selected_mask.change(
- fn=operations.update_brush_color,
- inputs=selected_mask,
- outputs=input_img,
- )
+ # Clean temp files
+ base = os.path.join(session.gradio_temp, "qim3d", session.username)
- # Make file download visible
- prep_dl_btn.click(
- fn=operations.save_mask,
- inputs=output_masks,
- outputs=[save_output, save_output],
- ).success(
- fn=lambda: os.remove('mask.tif')
- ) # Remove mask file from working directory immediately after sending it to /tmp/gradio
-
- # Update 'Add mask' button interactivit according to the current count
- counts.change(
- fn=operations.set_add_mask_btn_interactivity,
- inputs=counts,
- outputs=add_mask_btn,
- )
+ try:
+ files = os.listdir(base)
+ for filename in files:
+ # Check if "mask" is in the filename
+ if "mask" in filename:
+ file_path = os.path.join(base, filename)
+ os.remove(file_path)
- # Reset component configuration when image is cleared
- clear_img_btn.click(
- fn=operations.clear_img_update,
- inputs=None,
- outputs=[
- selected_mask,
- prep_dl_btn,
- save_output,
- counts,
- input_img,
- upload_img_btn,
- clear_img_btn,
- ]
- + output_masks,
- )
+ except FileNotFoundError:
+ files = None
- return gradio_interface
+ return session
+ def overlay_images(self, background, masks, alpha=0.5):
+ """Overlay multiple RGB masks onto an RGB background image using alpha blending.
-class Operations:
- def __init__(self, max_masks, cmy_hex):
- self.max_masks = max_masks
- self.cmy_hex = cmy_hex
+ Args:
+ background (numpy.ndarray): The background RGB image with shape (height, width, 3).
+ masks (numpy.ndarray): The RGB mask images with shape (num_masks, height, width, 3).
+ alpha (float, optional): The alpha value for blending. Defaults to 0.5.
- def update_masks(self, input_img, selected_mask, masks_state, file):
- # Binarize mask (it is not per default due to anti-aliasing)
- input_mask = input_img["mask"]
- input_mask[input_mask > 0] = 255
+ Returns:
+ numpy.ndarray: The composite image with overlaid masks.
- try:
- file_name = file.name
- except AttributeError:
- file_name = "nb_img"
-
- # Add new file to state dictionary when this function sees it first time
- if file_name not in masks_state.keys():
- masks_state[file_name] = [[] for _ in range(self.max_masks)]
-
- # Get index of currently selected and non-selected masks
- sel_mask_idx = int(selected_mask[-1]) - 1
- nonsel_mask_idxs = [
- mask_idx
- for mask_idx in list(range(self.max_masks))
- if mask_idx != sel_mask_idx
- ]
-
- # Add background to state first time function is invoked in current session
- if len(masks_state[file_name][0]) == 0:
- for i in range(len(masks_state[file_name])):
- masks_state[file_name][i].append(input_mask)
-
- # Check for discrepancy between what is drawn and what is shown as output masks
- masks_state_combined = 0
- for i in range(len(masks_state[file_name])):
- masks_state_combined += masks_state[file_name][i][-1]
- discrepancy = masks_state_combined != input_mask
- if np.any(discrepancy): # Correct discrepancy in output masks
- for i in range(self.max_masks):
- masks_state[file_name][i][-1][discrepancy] = 0
-
- # Add most recent change in input to currently selected mask
- mask2append = input_mask
- for mask_idx in nonsel_mask_idxs:
- mask2append -= masks_state[file_name][mask_idx][-1]
- masks_state[file_name][sel_mask_idx].append(mask2append)
-
- return [masks_state[file_name][i][-1] for i in range(self.max_masks)]
-
- def save_mask(self, *masks):
- # Go from multi-channel to single-channel mask
- stacked_masks = np.stack(masks, axis=-1)
- final_mask = np.zeros_like(masks[0])
- final_mask[np.where(stacked_masks == 255)[:2]] = (
- np.where(stacked_masks == 255)[-1] + 1
- )
+ Raises:
+ ValueError: If input images have different shapes.
- # Save output image in a temp space (and to current directory which is a bug)
- filename = "mask.tif"
- tifffile.imwrite(filename, final_mask)
+ Note:
+ - The function performs alpha blending to overlay the masks onto the background.
+ - It ensures that the background and masks have the same shape before blending.
+ - It calculates the maximum projection of the masks and blends them onto the background.
+ - Brightness outside the masks is adjusted to maintain consistency with the background.
+ """
- save_output_update = gr.File(visible=True)
+ # Igonore alpha in case its there
+ background = background[..., :3]
+ masks = masks[..., :3]
- return save_output_update, filename
+ # Ensure both images have the same shape
+ if background.shape != masks.shape:
+ raise ValueError("Input images must have the same shape")
- def increment_mask(self, counts):
- # increment count by 1
- counts += 1
- counts = int(counts)
+ # Perform alpha blending
+ masks_max_projection = np.amax(masks, axis=2)
+ masks_max_projection = np.stack((masks_max_projection,) * 3, axis=-1)
- counts_update = gr.Number(value=counts)
- selected_mask_update = gr.Radio(
- value=f"Mask {counts}", choices=[f"Mask {i+1}" for i in range(counts)]
- )
- output_masks_update = [gr.Image(visible=True)] * counts + [
- gr.Image(visible=False)
- ] * (self.max_masks - counts)
+ # Normalize if we have something
+ if np.max(masks_max_projection) > 0:
+ masks_max_projection = masks_max_projection / np.max(masks_max_projection)
- return [counts_update, selected_mask_update] + output_masks_update
+ composite = background * (1 - alpha) + masks * alpha
+ composite = np.clip(composite, 0, 255).astype("uint8")
- def update_brush_color(self, selected_mask):
- sel_mask_idx = int(selected_mask[-1]) - 1
- if sel_mask_idx < len(self.cmy_hex):
- input_img_update = gr.Image(brush_color=self.cmy_hex[sel_mask_idx])
- else:
- input_img_update = gr.Image(brush_color="#000000") # Return black brush
+ # Adjust brightness outside masks
+ composite = composite + (background * (1 - alpha)) * (1 - masks_max_projection)
- return input_img_update
+ return composite.astype("uint8")
- def set_add_mask_btn_interactivity(self, counts):
- add_mask_btn_update = (
- gr.Button(interactive=True)
- if counts < self.max_masks
- else gr.Button(interactive=False)
- )
- return add_mask_btn_update
-
- def clear_img_update(self):
- selected_mask_update = gr.Radio(
- choices=["Mask 1"], value="Mask 1"
- ) # Reset radio component to only show 'Mask 1'
- prep_dl_btn_update = gr.Button(
- visible=False
- ) # Make 'Prepare mask for download' button invisible
- save_output_update = gr.File(visible=False) # Make File save box invisible
- counts_update = gr.Number(value=1) # Reset invisible counter to 1
- input_img_update = gr.Image(
- value=None, interactive=False
- ) # Set input image component to non-interactive (so a new image cannot be uploaded directly in the component)
- upload_img_btn_update = gr.Button(
- interactive=True
- ) # Make 'Upload image' button interactive
- clear_img_btn_update = gr.Button(
- interactive=False
- ) # Make 'Clear image' button non-interactive
- output_masks_update = [
- gr.Image(value=None, visible=True if i == 0 else False, interactive=False)
- for i in range(self.max_masks)
- ] # Remove drawn masks and set as invisible except mask 1. 'interactive=False' added bc of bug after Gradio 3.44.x
-
- return [
- selected_mask_update,
- prep_dl_btn_update,
- save_output_update,
- counts_update,
- input_img_update,
- upload_img_btn_update,
- clear_img_btn_update,
- ] + output_masks_update
-
- def upload_img_update(self, file):
- input_img_update = gr.Image(
- value=load(file.name), interactive=True
- ) # Upload image from button to Image components
- clear_img_btn_update = gr.Button(
- interactive=True
- ) # Make 'Clear image' button interactive
- upload_img_btn_update = gr.Button(
- interactive=False
- ) # Make 'Upload image' button non-interactive
- prep_dl_btn_update = gr.Button(
- visible=True
- ) # Make 'Prepare mask for download' button visible
- output_masks_update = [
- gr.Image(interactive=True)
- ] * self.max_masks # This line is added bc of bug in Gradio after 3.44.x
-
- return [
- input_img_update,
- clear_img_btn_update,
- upload_img_btn_update,
- prep_dl_btn_update,
- ] + output_masks_update
-
-
-def run_interface(host = "0.0.0.0"):
+ def preview(self, session):
+ background = session.img_editor["background"]
+ masks = session.img_editor["layers"][0]
+ overlay_image = qim3d.utils.img.overlay_rgb_images(background, masks)
+
+ return overlay_image
+
+ def separate_masks(self, session):
+
+ masks_rgb = session.img_editor["layers"][0]
+ mask_threshold = 200 # This value is based
+
+ mask_list = []
+ files_list = []
+
+ # Go through each channel
+ for idx in np.arange(session.n_masks):
+
+ mask_grayscale = masks_rgb[:, :, idx]
+ mask = mask_grayscale > mask_threshold
+
+ # Save only if we have a mask
+ if np.sum(mask) > 0:
+ mask_list.append(mask)
+ filename = f"mask_{session.mask_names[idx]}.tif"
+ base = os.path.join(session.gradio_temp, "qim3d", session.username)
+ if not os.path.exists(base):
+ os.makedirs(base)
+ filepath = os.path.join(base, filename)
+ files_list.append(filepath)
+
+ save(filepath, mask, replace=True)
+ session.temp_files.append(filepath)
+
+ return session, files_list
+
+
+def run_interface(host="0.0.0.0"):
gradio_interface = Interface().create_interface()
- internal_tools.run_gradio_app(gradio_interface,host)
+ qim3d.utils.internal_tools.run_gradio_app(gradio_interface, host)
+
if __name__ == "__main__":
# Creates interface
- run_interface()
\ No newline at end of file
+ run_interface()
diff --git a/qim3d/utils/__init__.py b/qim3d/utils/__init__.py
index 2d665cda..f3cd4eb1 100644
--- a/qim3d/utils/__init__.py
+++ b/qim3d/utils/__init__.py
@@ -4,4 +4,5 @@ from .augmentations import Augmentation
from .data import Dataset, prepare_datasets, prepare_dataloaders
#from .doi import get_bibtex, get_reference
from . import doi
-from .system import Memory
\ No newline at end of file
+from .system import Memory
+from .img import overlay_rgb_images
\ No newline at end of file
diff --git a/qim3d/utils/img.py b/qim3d/utils/img.py
new file mode 100644
index 00000000..f485c13e
--- /dev/null
+++ b/qim3d/utils/img.py
@@ -0,0 +1,46 @@
+import numpy as np
+
+def overlay_rgb_images(background, foreground, alpha=0.5):
+ """Overlay multiple RGB foreground onto an RGB background image using alpha blending.
+
+ Args:
+ background (numpy.ndarray): The background RGB image.
+ foreground (numpy.ndarray): The foreground RGB image (usually masks).
+ alpha (float, optional): The alpha value for blending. Defaults to 0.5.
+
+ Returns:
+ numpy.ndarray: The composite RGB image with overlaid foreground.
+
+ Raises:
+ ValueError: If input images have different shapes.
+
+ Note:
+ - The function performs alpha blending to overlay the foreground onto the background.
+ - It ensures that the background and foreground have the same shape before blending.
+ - It calculates the maximum projection of the foreground and blends them onto the background.
+ - Brightness outside the foreground is adjusted to maintain consistency with the background.
+ """
+
+ # Igonore alpha in case its there
+ background = background[..., :3]
+ foreground = foreground[..., :3]
+
+ # Ensure both images have the same shape
+ if background.shape != foreground.shape:
+ raise ValueError("Input images must have the same shape")
+
+ # Perform alpha blending
+ foreground_max_projection = np.amax(foreground, axis=2)
+ foreground_max_projection = np.stack((foreground_max_projection,) * 3, axis=-1)
+
+ # Normalize if we have something
+ if np.max(foreground_max_projection) > 0:
+ foreground_max_projection = foreground_max_projection / np.max(foreground_max_projection)
+
+ composite = background * (1 - alpha) + foreground * alpha
+ composite = np.clip(composite, 0, 255).astype("uint8")
+
+ # Adjust brightness outside foreground
+ composite = composite + (background * (1 - alpha)) * (1 - foreground_max_projection)
+
+ return composite.astype("uint8")
--
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