now supports url parameters and example in the app

README.md

@@ -1,23 +1,9 @@
----
-title: Pystackreg Web App
-emoji: 🧠
-colorFrom: indigo
-colorTo: blue
-sdk: gradio
-sdk_version: 5.25.1
-app_file: app.py
-pinned: false
-tags:
-  - image-processing
-  - registration
-  - pystackreg
----
 # 🧠 Stack Image Registration Web App  
 A web-based application for image stack registration powered by **Gradio** and **pystackreg**.  
 This tool allows users to align and stabilize multi-frame TIFF images using a variety of transformation models.
 
 <p align="center">
-    <img src="https://raw.githubusercontent.com/qchapp/pystackreg-app/refs/heads/master/images/app.png" height="500">
+    <img src="images/app.png" height="500">
 </p>
 
 ---
@@ -83,6 +69,45 @@ Each mode offers:
 
 ---
 
+### 📂 Examples in the App
+
+You can try the application directly using preloaded examples from the [`pystackreg`](https://github.com/glichtner/pystackreg) repository.  
+Each mode includes interactive buttons that load demo TIFF stacks automatically:
+
+- 📚 **Reference-Based Alignment**:  
+  Loads a stack of PC12 microscopy frames.
+
+- 🎯 **Stack-Based Alignment**:  
+  Loads both an unregistered and a translation-aligned stack.
+
+- 🧩 **Frame-to-Frame Alignment**:  
+  Uses the same unregistered stack for aligning specific frames.
+
+No need to upload your own files — just click and experiment!
+
+---
+
+### 🌐 URL Parameter Support
+
+The app supports loading image stacks from external URLs using query parameters.
+
+**▶️ Load a single stack (for Reference-Based or Frame-to-Frame):**
+
+```
+https://huggingface.co/spaces/qchapp/pystackreg-app?file_url=https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-unreg.tif
+```
+
+
+**▶️ Load two stacks (for Stack-Based Alignment):**
+
+```
+https://huggingface.co/spaces/qchapp/pystackreg-app?file_url_1=https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-unreg.tif&file_url_2=https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-reg-translation.tif
+```
+
+> 💡 The app will automatically load and preview the provided stack(s) in the appropriate tabs.
+
+---
+
 ### 📚 Credits
 
 - **App Author**: [Quentin Chappuis](https://github.com/qchapp)  

app.py

@@ -5,6 +5,7 @@ from pystackreg import StackReg
 import imageio.v2 as iio
 import tifffile
 import tempfile
+import urllib.request
 
 from core.utils import *
 
@@ -12,38 +13,34 @@ from core.utils import *
 original_frames, aligned_frames = [], []
 ref_frames, mov_frames, reg_frames = [], [], []
 custom_stack, reg_result = [], None
-full_stack, full_aligned = [], []
 
-# reset
+# Reset functions
 def reset_intra_stack():
     global original_frames, aligned_frames
     original_frames, aligned_frames = [], []
-    return [None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0), None]
+    return [None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0),
+            None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0), None]
 
 def reset_reference_based():
     global ref_frames, mov_frames, reg_frames
     ref_frames, mov_frames, reg_frames = [], [], []
-    return [None, None, None, gr.update(value=0, minimum=0, maximum=0), None, gr.update(value=0, minimum=0, maximum=0), None]
+    return [None, None, None, gr.update(value=0, minimum=0, maximum=0),
+            None, gr.update(value=0, minimum=0, maximum=0), None]
 
 def reset_frame_to_frame():
     global custom_stack, reg_result
     custom_stack, reg_result = [], None
-    return [None, gr.update(value=0, minimum=0, maximum=0), gr.update(value=0, minimum=0, maximum=0), None, None]
+    return [None, gr.update(value=0, minimum=0, maximum=0),
+            gr.update(value=0, minimum=0, maximum=0), None, None]
 
-
-# Registration Logic
+# Registration logic
 def intra_stack_align(f, ref_idx, ext_file, ext_idx, mode):
     global original_frames, aligned_frames
     stack = load_stack(f)
     original_frames = [Image.fromarray(fr) for fr in stack]
     sr = StackReg(get_sr_mode(mode))
 
-    if ext_file:
-        ext_stack = load_stack(ext_file)
-        ref = ext_stack[ext_idx]
-    else:
-        ref = stack[ref_idx]
-
+    ref = load_stack(ext_file)[ext_idx] if ext_file else stack[ref_idx]
     aligned = [sr.register_transform(ref, fr) for fr in stack]
     aligned = normalize_stack(np.stack(aligned))
     aligned_frames = [upscale(Image.fromarray(fr)) for fr in aligned]
@@ -52,11 +49,8 @@ def intra_stack_align(f, ref_idx, ext_file, ext_idx, mode):
     tifffile.imwrite(path, aligned, photometric='minisblack')
 
     return (
-        original_frames[0],
-        gr.update(value=0, maximum=len(original_frames) - 1),
-        aligned_frames[0],
-        gr.update(value=0, maximum=len(aligned_frames) - 1),
-        path
+        original_frames[0], gr.update(value=0, maximum=len(original_frames)-1),
+        aligned_frames[0], gr.update(value=0, maximum=len(aligned_frames)-1), path
     )
 
 def reference_align(ref_file, mov_file, mode):
@@ -65,10 +59,12 @@ def reference_align(ref_file, mov_file, mode):
     mov_stack = load_stack(mov_file)
     ref_frames = [Image.fromarray(f) for f in ref_stack]
     mov_frames = [Image.fromarray(f) for f in mov_stack]
+
     sr = StackReg(get_sr_mode(mode))
     aligned = [sr.register_transform(ref_stack[0], f) for f in mov_stack]
     aligned = normalize_stack(np.stack(aligned))
     reg_frames = [upscale(Image.fromarray(f)) for f in aligned]
+
     path = tempfile.NamedTemporaryFile(suffix=".tif", delete=False).name
     tifffile.imwrite(path, aligned, photometric='minisblack')
     return ref_frames[0], gr.update(value=0, maximum=len(ref_frames)-1), \
@@ -78,14 +74,28 @@ def frame_to_frame_align(file, ref_idx, mov_idx, mode):
     global custom_stack, reg_result
     stack = load_stack(file)
     custom_stack = [Image.fromarray(f) for f in stack]
+
     sr = StackReg(get_sr_mode(mode))
     aligned = sr.register_transform(stack[ref_idx], stack[mov_idx])
     aligned = normalize_stack(np.stack([aligned]))[0]
     reg_result = Image.fromarray(aligned)
+
     path = tempfile.NamedTemporaryFile(suffix=".tif", delete=False).name
     tifffile.imwrite(path, aligned[np.newaxis, ...], photometric='minisblack')
     return reg_result, path
 
+# URL loading
+def load_from_url(request: gr.Request):
+    params = request.query_params
+    if "file_url" in params:
+        try:
+            url = params["file_url"]
+            tmp_path = tempfile.mktemp(suffix=".tif")
+            urllib.request.urlretrieve(url, tmp_path)
+            return [gr.update(value=tmp_path)]
+        except Exception as e:
+            print(f"[URL load failed] {e}")
+    return [None]
 
 # Interface
 with gr.Blocks() as demo:
@@ -100,16 +110,24 @@ with gr.Blocks() as demo:
             file_input = gr.File(label="Upload Stack to Register")
             use_ext_ref = gr.Checkbox(label="Use external reference stack")
 
+        gr.Examples(
+            examples=[
+                ["https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-unreg.tif"]
+            ],
+            inputs=[file_input],
+            label="Try with Example TIFF"
+        )
+
         with gr.Row():
             ref_slider = gr.Slider(label="Reference Frame (from uploaded stack)", minimum=0, maximum=0, value=0, step=1, visible=True)
             ext_ref_file = gr.File(label="Upload External Reference Stack (.tif)", visible=False)
             ext_ref_slider = gr.Slider(label="Reference Frame (from external stack)", minimum=0, maximum=0, value=0, step=1, visible=False)
 
         use_ext_ref.change(
-            lambda use_ext: (
-                gr.update(visible=not use_ext),
-                gr.update(visible=use_ext),
-                gr.update(visible=use_ext)
+            lambda v: (
+                gr.update(visible=not v),
+                gr.update(visible=v),
+                gr.update(visible=v)
             ),
             use_ext_ref,
             [ref_slider, ext_ref_file, ext_ref_slider]
@@ -122,11 +140,11 @@ with gr.Blocks() as demo:
         )
 
         with gr.Row():
-            show_advanced = gr.Checkbox(label="Show Advanced Settings", value=False)
+            show_adv = gr.Checkbox(label="Show Advanced Settings", value=False)
             mode_dropdown = gr.Dropdown(["TRANSLATION", "RIGID_BODY", "SCALED_ROTATION", "AFFINE", "BILINEAR"],
-                                        value="RIGID_BODY", label="Transformation Mode", visible=False)
+                                        value="RIGID_BODY", visible=False, label="Transformation Mode")
 
-        show_advanced.change(lambda v: gr.update(visible=v), show_advanced, mode_dropdown)
+        show_adv.change(lambda v: gr.update(visible=v), show_adv, mode_dropdown)
         run_btn = gr.Button("▶️ Align Stack")
 
         with gr.Row():
@@ -151,11 +169,12 @@ with gr.Blocks() as demo:
             [original_image, original_slider, aligned_image, aligned_slider, download]
         )
 
-        original_slider.change(lambda i: original_frames[i] if 0 <= i < len(original_frames) else None, original_slider, original_image)
-        aligned_slider.change(lambda i: aligned_frames[i] if 0 <= i < len(aligned_frames) else None, aligned_slider, aligned_image)
+        original_slider.change(lambda i: original_frames[i] if 0 <= i < len(original_frames) else None,
+                               original_slider, original_image)
+        aligned_slider.change(lambda i: aligned_frames[i] if 0 <= i < len(aligned_frames) else None,
+                              aligned_slider, aligned_image)
 
-        reset_btn = gr.Button("🔄 Reset Tab")
-        reset_btn.click(
+        gr.Button("🔄 Reset Tab").click(
             reset_intra_stack,
             outputs=[
                 file_input, ref_slider, ext_ref_file, ext_ref_slider,
@@ -168,10 +187,21 @@ with gr.Blocks() as demo:
             ref_input = gr.File(label="Reference Stack")
             mov_input = gr.File(label="Moving Stack")
 
+        gr.Examples(
+            examples=[
+                [
+                    "https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-unreg.tif",
+                    "https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-reg-translation.tif"
+                ]
+            ],
+            inputs=[ref_input, mov_input],
+            label="Try with Example Stacks"
+        )
+
         with gr.Row():
             show_adv_ref = gr.Checkbox(label="Show Advanced Settings", value=False)
             mode_dropdown_ref = gr.Dropdown(["TRANSLATION", "RIGID_BODY", "SCALED_ROTATION", "AFFINE", "BILINEAR"],
-                                            value="RIGID_BODY", label="Transformation Mode", visible=False)
+                                            value="RIGID_BODY", visible=False, label="Transformation Mode")
 
         show_adv_ref.change(lambda v: gr.update(visible=v), show_adv_ref, mode_dropdown_ref)
         ref_btn = gr.Button("▶️ Register")
@@ -191,23 +221,30 @@ with gr.Blocks() as demo:
         ref_slider.change(lambda i: ref_frames[i] if 0 <= i < len(ref_frames) else None, ref_slider, ref_image)
         reg_slider.change(lambda i: reg_frames[i] if 0 <= i < len(reg_frames) else None, reg_slider, reg_image)
 
-        reset_ref_btn = gr.Button("🔄 Reset Tab")
-        reset_ref_btn.click(
+        gr.Button("🔄 Reset Tab").click(
             reset_reference_based,
             outputs=[ref_input, mov_input, ref_image, ref_slider, reg_image, reg_slider, download_ref]
         )
 
-
     with gr.Tab("🧩 Frame-to-Frame Alignment"):
         with gr.Row():
             frame_file = gr.File(label="Upload Stack")
             ref_idx = gr.Slider(label="Reference Frame", minimum=0, maximum=0, value=0, step=1)
             mov_idx = gr.Slider(label="Moving Frame", minimum=0, maximum=0, value=0, step=1)
 
+        gr.Examples(
+            examples=[
+                ["https://github.com/glichtner/pystackreg/raw/master/examples/data/pc12-unreg.tif"]
+            ],
+            inputs=[frame_file],
+            label="Try with Example Stack"
+        )
+
+
         with gr.Row():
             show_adv_ftf = gr.Checkbox(label="Show Advanced Settings", value=False)
             mode_dropdown_ftf = gr.Dropdown(["TRANSLATION", "RIGID_BODY", "SCALED_ROTATION", "AFFINE", "BILINEAR"],
-                                            value="RIGID_BODY", label="Transformation Mode", visible=False)
+                                            value="RIGID_BODY", visible=False, label="Transformation Mode")
 
         show_adv_ftf.change(lambda v: gr.update(visible=v), show_adv_ftf, mode_dropdown_ftf)
         frame_btn = gr.Button("▶️ Register Frame")
@@ -215,16 +252,59 @@ with gr.Blocks() as demo:
         download_ftf = gr.File(label="Download")
 
         frame_file.change(
-            lambda f: [gr.update(value=0, maximum=len(iio.mimread(f)) - 1)]*2 if f else [gr.update(value=0, maximum=0)]*2,
+            lambda f: [gr.update(value=0, maximum=len(iio.mimread(f)) - 1)] * 2 if f else [gr.update(value=0, maximum=0)] * 2,
             frame_file, [ref_idx, mov_idx]
         )
-        frame_btn.click(frame_to_frame_align, [frame_file, ref_idx, mov_idx, mode_dropdown_ftf], [frame_output, download_ftf])
 
-        reset_ftf_btn = gr.Button("🔄 Reset Tab")
-        reset_ftf_btn.click(
+        frame_btn.click(frame_to_frame_align,
+                        [frame_file, ref_idx, mov_idx, mode_dropdown_ftf],
+                        [frame_output, download_ftf])
+
+        gr.Button("🔄 Reset Tab").click(
             reset_frame_to_frame,
             outputs=[frame_file, ref_idx, mov_idx, frame_output, download_ftf]
         )
 
+    @demo.load(
+        outputs=[file_input, ref_slider, frame_file, ref_idx, mov_idx, ref_input, mov_input]
+    )
+    def load_from_query(request: gr.Request):
+        params = request.query_params
+        results = [None] * 7  # 7 outputs
+
+        # One-stack file case (for ref-based + frame-to-frame)
+        if "file_url" in params:
+            try:
+                url = params["file_url"]
+                tmp_path = tempfile.mktemp(suffix=".tif")
+                urllib.request.urlretrieve(url, tmp_path)
+                stack = iio.mimread(tmp_path)
+                max_frame = len(stack) - 1
+
+                results[0] = tmp_path  # file_input
+                results[1] = gr.update(value=0, maximum=max_frame)  # ref_slider
+                results[2] = tmp_path  # frame_file
+                results[3] = gr.update(value=0, maximum=max_frame)  # ref_idx
+                results[4] = gr.update(value=1 if max_frame >= 1 else 0, maximum=max_frame)  # mov_idx
+
+            except Exception as e:
+                print(f"[Error loading file_url] {e}")
+
+        # Two-stack file case (for stack-based alignment)
+        if "file_url_1" in params and "file_url_2" in params:
+            try:
+                tmp_path_1 = tempfile.mktemp(suffix=".tif")
+                tmp_path_2 = tempfile.mktemp(suffix=".tif")
+                urllib.request.urlretrieve(params["file_url_1"], tmp_path_1)
+                urllib.request.urlretrieve(params["file_url_2"], tmp_path_2)
+                results[5] = tmp_path_1  # ref_input
+                results[6] = tmp_path_2  # mov_input
+            except Exception as e:
+                print(f"[Error loading file_url_1 or file_url_2] {e}")
+
+        return results
+
+
+
 if __name__ == "__main__":
     demo.launch()