celldetective 1.5.0b4__py3-none-any.whl → 1.5.0b6__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.5.0b4"
+__version__ = "1.5.0b6"

celldetective/gui/base/figure_canvas.py

@@ -22,19 +22,33 @@ class FigureCanvas(CelldetectiveWidget):
             from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT
 
             self.toolbar = NavigationToolbar2QT(self.canvas)
+            self.toolbar.setStyleSheet(
+                "QToolButton:hover {background-color: lightgray;} QToolButton {background-color: transparent; border: none;}"
+            )
         self.layout = QVBoxLayout(self)
         self.layout.addWidget(self.canvas, 90)
         if interactive:
             self.layout.addWidget(self.toolbar)
 
-        #center_window(self)
+        self.manual_layout = False
+        # center_window(self)
         self.setAttribute(Qt.WA_DeleteOnClose)
 
     def resizeEvent(self, event):
-
+        print("DEBUG: resizeEvent called")
         super().resizeEvent(event)
         try:
-            self.fig.tight_layout()
+            manual_layout = getattr(self, "manual_layout", False)
+
+            # Double check for profile axes manually (robust fallback)
+            if not manual_layout and hasattr(self.fig, "axes"):
+                for ax in self.fig.axes:
+                    if ax.get_label() == "profile_axes":
+                        manual_layout = True
+                        break
+
+            if not manual_layout:
+                self.fig.tight_layout()
         except:
             pass
 

celldetective/gui/viewers/base_viewer.py

@@ -285,6 +285,10 @@ class StackVisualizer(CelldetectiveWidget):
             self.lock_y_action.setEnabled(True)
             self.canvas.toolbar.mode = ""
 
+            # Enable manual layout control to prevent tight_layout interference
+            if hasattr(self.canvas, "manual_layout"):
+                self.canvas.manual_layout = True
+
             # Connect events
             self.cid_press = self.fig.canvas.mpl_connect(
                 "button_press_event", self.on_line_press
@@ -297,8 +301,8 @@ class StackVisualizer(CelldetectiveWidget):
             )
 
             # Save original position if not saved
-            if not hasattr(self, "ax_original_pos"):
-                self.ax_original_pos = self.ax.get_position()
+            # if not hasattr(self, "ax_original_pos"):
+            #     self.ax_original_pos = self.ax.get_position()
 
             # Disable tight_layout/layout engine to prevent fighting manual positioning
             if hasattr(self.fig, "set_layout_engine"):
@@ -334,6 +338,7 @@ class StackVisualizer(CelldetectiveWidget):
                 self.ax_profile.set_position(gs[1].get_position(self.fig))
 
             self.ax_profile.set_visible(True)
+            self.ax_profile.set_label("profile_axes")
             self.ax_profile.set_facecolor("none")
             self.ax_profile.tick_params(axis="y", which="major", labelsize=8)
             self.ax_profile.set_xticks([])
@@ -346,11 +351,40 @@ class StackVisualizer(CelldetectiveWidget):
             self.ax_profile.spines["bottom"].set_color("black")
             self.ax_profile.spines["left"].set_color("black")
 
+            # Update Toolbar Home State to match new layout BUT with full field of view
+            # 1. Save current zoom
+            current_xlim = self.ax.get_xlim()
+            current_ylim = self.ax.get_ylim()
+
+            # 2. Set limits to full extent (Home State)
+            if hasattr(self, "im"):
+                extent = self.im.get_extent()  # (left, right, bottom, top) or similar
+                self.ax.set_xlim(extent[0], extent[1])
+                self.ax.set_ylim(extent[2], extent[3])
+
+            # 3. Reset Stack and save Home
+            self.canvas.toolbar._nav_stack.clear()
+            self.canvas.toolbar.push_current()
+
+            # 4. Restore User Zoom
+            self.ax.set_xlim(current_xlim)
+            self.ax.set_ylim(current_ylim)
+
+            # 5. Push restored zoom state so "Back"/"Forward" logic works from here?
+            # Actually, if we just restore, we are "live" at a new state.
+            # If we don't push, "Home" works. "Back" might not exist yet. That's fine.
+            self.canvas.toolbar.push_current()
+
             self.canvas.draw()
         else:
             self.line_mode = False
             self.lock_y_action.setChecked(False)
             self.lock_y_action.setEnabled(False)
+
+            # Disable manual layout control
+            if hasattr(self.canvas, "manual_layout"):
+                self.canvas.manual_layout = False
+
             # Disconnect events
             if hasattr(self, "cid_press"):
                 self.fig.canvas.mpl_disconnect(self.cid_press)
@@ -372,17 +406,24 @@ class StackVisualizer(CelldetectiveWidget):
                 self.ax_profile = None
 
             # Restore original layout
-            if hasattr(self, "ax_original_pos"):
-                # standard 1x1 GridSpec or manual restore
-                import matplotlib.gridspec as gridspec
-
-                gs = gridspec.GridSpec(1, 1)
-                self.ax.set_subplotspec(gs[0])
-                self.ax.set_position(gs[0].get_position(self.fig))
-                self.fig.subplots_adjust(
-                    top=1, bottom=0, right=1, left=0, hspace=0, wspace=0
-                )
-                # self.ax.set_position(self.ax_original_pos) # tight layout should fix it
+            # if hasattr(self, "ax_original_pos"):
+            # standard 1x1 GridSpec or manual restore
+            import matplotlib.gridspec as gridspec
+
+            gs = gridspec.GridSpec(1, 1)
+            self.ax.set_subplotspec(gs[0])
+            # self.ax.set_position(gs[0].get_position(self.fig))
+            self.fig.subplots_adjust(
+                top=1, bottom=0, right=1, left=0, hspace=0, wspace=0
+            )
+            # self.ax.set_position(self.ax_original_pos) # tight layout should fix it
+
+            # Re-enable tight_layout via standard resize event later or explicit call
+            self.fig.tight_layout()
+
+            # Reset Toolbar Stack for Standard View
+            self.canvas.toolbar._nav_stack.clear()
+            self.canvas.toolbar.push_current()
 
             self.canvas.draw()
             self.info_lbl.setText("")
@@ -553,7 +594,10 @@ class StackVisualizer(CelldetectiveWidget):
             self.mode = "direct"
             self.stack_length = len(self.stack)
             self.mid_time = self.stack_length // 2
-            self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+            self.current_time_index = 0
+            self.init_frame = self.stack[
+                self.current_time_index, :, :, self.target_channel
+            ]
             self.last_frame = self.stack[-1, :, :, self.target_channel]
         else:
             self.mode = "virtual"
@@ -566,6 +610,7 @@ class StackVisualizer(CelldetectiveWidget):
 
         self.stack_length = auto_load_number_of_frames(self.stack_path)
         self.mid_time = self.stack_length // 2
+        self.current_time_index = 0
         self.img_num_per_channel = _get_img_num_per_channel(
             np.arange(self.n_channels), self.stack_length, self.n_channels
         )
@@ -578,7 +623,7 @@ class StackVisualizer(CelldetectiveWidget):
         self.loader_thread.start()
 
         self.init_frame = load_frames(
-            self.img_num_per_channel[self.target_channel, self.mid_time],
+            self.img_num_per_channel[self.target_channel, self.current_time_index],
             self.stack_path,
             normalize_input=False,
         )[:, :, 0]
@@ -713,7 +758,7 @@ class StackVisualizer(CelldetectiveWidget):
         layout = QHBoxLayout()
         self.frame_slider = QLabeledSlider(Qt.Horizontal)
         self.frame_slider.setRange(0, self.stack_length - 1)
-        self.frame_slider.setValue(self.mid_time)
+        self.frame_slider.setValue(self.current_time_index)
         self.frame_slider.valueChanged.connect(self.change_frame)
         layout.addWidget(QLabel("Time: "), 15)
         layout.addWidget(self.frame_slider, 85)
@@ -721,7 +766,7 @@ class StackVisualizer(CelldetectiveWidget):
 
     def set_target_channel(self, value):
         self.target_channel = value
-        self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+        self.init_frame = self.stack[self.current_time_index, :, :, self.target_channel]
         self.im.set_data(self.init_frame)
         self.canvas.draw()
         self.update_profile()
@@ -739,7 +784,9 @@ class StackVisualizer(CelldetectiveWidget):
             self.change_frame_from_channel_switch(self.frame_slider.value())
         else:
             if self.stack is not None and self.stack.ndim == 4:
-                self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+                self.init_frame = self.stack[
+                    self.current_time_index, :, :, self.target_channel
+                ]
                 self.im.set_data(self.init_frame)
                 self.canvas.draw()
                 self.update_profile()
@@ -752,7 +799,8 @@ class StackVisualizer(CelldetectiveWidget):
             p01 = np.nanpercentile(self.init_frame, 0.1)
             p99 = np.nanpercentile(self.init_frame, 99.9)
             self.im.set_clim(vmin=p01, vmax=p99)
-            self.contrast_slider.setValue((p01, p99))
+            if self.create_contrast_slider and hasattr(self, "contrast_slider"):
+                self.contrast_slider.setValue((p01, p99))
             self.channel_trigger = False
             self.canvas.draw()
 
@@ -831,6 +879,14 @@ class StackVisualizer(CelldetectiveWidget):
         # Event handler for closing the widget
         if self.loader_thread:
             self.loader_thread.stop()
+            self.loader_thread = None
         if hasattr(self, "frame_cache") and isinstance(self.frame_cache, OrderedDict):
             self.frame_cache.clear()
         self.canvas.close()
+
+    def __del__(self):
+        try:
+            if hasattr(self, "loader_thread") and self.loader_thread:
+                self.loader_thread.stop()
+        except:
+            pass

celldetective/gui/viewers/channel_offset_viewer.py

@@ -9,11 +9,16 @@ from superqt import QLabeledDoubleSlider, QLabeledDoubleRangeSlider
 from celldetective.gui.base.components import QHSeperationLine
 from celldetective.gui.gui_utils import QuickSliderLayout, ThresholdLineEdit
 from celldetective.gui.viewers.base_viewer import StackVisualizer
-from celldetective.utils.image_loaders import load_frames, auto_load_number_of_frames, _get_img_num_per_channel
+from celldetective.utils.image_loaders import (
+    load_frames,
+    auto_load_number_of_frames,
+    _get_img_num_per_channel,
+)
 from celldetective import get_logger
 
 logger = get_logger(__name__)
 
+
 class ChannelOffsetViewer(StackVisualizer):
 
     def __init__(self, parent_window=None, *args, **kwargs):
@@ -22,16 +27,32 @@ class ChannelOffsetViewer(StackVisualizer):
         self.overlay_target_channel = -1
         self.shift_vertical = 0
         self.shift_horizontal = 0
+        self.overlay_init_contrast = False
         super().__init__(*args, **kwargs)
 
         self.load_stack()
+
+        if self.mode == "direct":
+            # Initialize overlay frames for direct mode
+            default_overlay_idx = -1
+            if self.stack.ndim == 4:
+                self.overlay_init_frame = self.stack[
+                    self.current_time_index, :, :, default_overlay_idx
+                ]
+                self.overlay_last_frame = self.stack[-1, :, :, default_overlay_idx]
+            else:
+                # Should rely on 4D stack assumption from StackVisualizer
+                self.overlay_init_frame = self.init_frame
+                self.overlay_last_frame = self.last_frame
+
         self.canvas.layout.addWidget(QHSeperationLine())
 
         self.generate_overlay_channel_cb()
         self.generate_overlay_imshow()
 
         self.generate_overlay_alpha_slider()
-        self.generate_overlay_contrast_slider()
+        if self.create_contrast_slider:
+            self.generate_overlay_contrast_slider()
 
         self.generate_overlay_shift()
         self.generate_add_to_parent_btn()
@@ -190,7 +211,7 @@ class ChannelOffsetViewer(StackVisualizer):
 
         self.im_overlay.set_data(self.overlay_init_frame)
 
-        if self.overlay_init_contrast:
+        if self.overlay_init_contrast and self.create_contrast_slider:
             self.im_overlay.autoscale()
             I_min, I_max = self.im_overlay.get_clim()
             self.overlay_contrast_slider.setRange(
@@ -214,12 +235,13 @@ class ChannelOffsetViewer(StackVisualizer):
             gc.collect()
 
         self.mid_time = self.stack_length // 2
+        self.current_time_index = 0
         self.img_num_per_channel = _get_img_num_per_channel(
             np.arange(self.n_channels), self.stack_length, self.n_channels
         )
 
         self.init_frame = load_frames(
-            self.img_num_per_channel[self.target_channel, self.mid_time],
+            self.img_num_per_channel[self.target_channel, self.current_time_index],
             self.stack_path,
             normalize_input=False,
         ).astype(float)[:, :, 0]
@@ -229,7 +251,9 @@ class ChannelOffsetViewer(StackVisualizer):
             normalize_input=False,
         ).astype(float)[:, :, 0]
         self.overlay_init_frame = load_frames(
-            self.img_num_per_channel[self.overlay_target_channel, self.mid_time],
+            self.img_num_per_channel[
+                self.overlay_target_channel, self.current_time_index
+            ],
             self.stack_path,
             normalize_input=False,
         ).astype(float)[:, :, 0]
@@ -306,6 +330,7 @@ class ChannelOffsetViewer(StackVisualizer):
         )
         self.im_overlay.set_data(self.shifted_frame)
         self.fig.canvas.draw_idle()
+        self.update_profile()
 
     def generate_add_to_parent_btn(self):
 
@@ -318,6 +343,95 @@ class ChannelOffsetViewer(StackVisualizer):
         add_hbox.addWidget(QLabel(""), 33)
         self.canvas.layout.addLayout(add_hbox)
 
+    def update_profile(self):
+        if not self.line_mode or not hasattr(self, "line_x") or not self.line_x:
+            return
+
+        # Calculate profile
+        x0, y0 = self.line_x[0], self.line_y[0]
+        x1, y1 = self.line_x[1], self.line_y[1]
+        length_px = np.hypot(x1 - x0, y1 - y0)
+        if length_px == 0:
+            return
+
+        num_points = int(length_px)
+        if num_points < 2:
+            num_points = 2
+
+        x, y = np.linspace(x0, x1, num_points), np.linspace(y0, y1, num_points)
+
+        # Use self.init_frame and overlay frame
+        profiles = []
+        colors = ["black", "tab:blue"]
+
+        # Main channel profile
+        if hasattr(self, "init_frame") and self.init_frame is not None:
+            from scipy.ndimage import map_coordinates
+
+            profile = map_coordinates(
+                self.init_frame, np.vstack((y, x)), order=1, mode="nearest"
+            )
+            profiles.append(profile)
+        else:
+            profiles.append(None)
+
+        # Overlay channel profile
+        # Use data currently in im_overlay, which accounts for shifts
+        overlay_data = self.im_overlay.get_array()
+        if overlay_data is not None:
+            from scipy.ndimage import map_coordinates
+
+            profile_overlay = map_coordinates(
+                overlay_data, np.vstack((y, x)), order=1, mode="nearest"
+            )
+            profiles.append(profile_overlay)
+        else:
+            profiles.append(None)
+
+        # Basic setup
+        self.ax_profile.clear()
+        self.ax_profile.set_facecolor("none")
+
+        # Distance axis
+        dist_axis = np.arange(num_points)
+        title_str = f"{round(length_px,2)} [px]"
+        if self.PxToUm is not None:
+            title_str += f" | {round(length_px*self.PxToUm,3)} [µm]"
+
+        # Handle Y-Axis Locking
+        current_ylim = None
+        if self.lock_y_action.isChecked():
+            current_ylim = self.ax_profile.get_ylim()
+
+        # Plot profiles
+        for i, (profile, color) in enumerate(zip(profiles, colors)):
+            if profile is not None:
+                if np.all(np.isnan(profile)):
+                    profile = np.zeros_like(profile)
+                    profile[:] = np.nan
+
+                self.ax_profile.plot(
+                    dist_axis, profile, color=color, linestyle="-", label=f"Ch{i}"
+                )
+
+        self.ax_profile.set_xticks([])
+        self.ax_profile.set_ylabel("Intensity", fontsize=8)
+        self.ax_profile.set_xlabel(title_str, fontsize=8)
+        self.ax_profile.tick_params(axis="y", which="major", labelsize=6)
+
+        # Hide spines
+        self.ax_profile.spines["top"].set_visible(False)
+        self.ax_profile.spines["right"].set_visible(False)
+        self.ax_profile.spines["bottom"].set_color("black")
+        self.ax_profile.spines["left"].set_color("black")
+
+        self.fig.set_facecolor("none")
+
+        if current_ylim:
+            self.ax_profile.set_ylim(current_ylim)
+
+        self.fig.canvas.draw_idle()
+
     def set_parent_attributes(self):
 
         idx = self.channels_overlay_cb.currentIndex()

celldetective/gui/viewers/threshold_viewer.py

@@ -65,8 +65,6 @@ class ThresholdedStackVisualizer(StackVisualizer):
         self.thresh_min = 0.0
         self.thresh_max = 30.0
 
-        self.thresh_max = 30.0
-
         # Cache for processed images
         self.processed_cache = OrderedDict()
         self.processed_image = None
@@ -74,6 +72,15 @@ class ThresholdedStackVisualizer(StackVisualizer):
 
         self.generate_threshold_slider()
 
+        # Ensure we start at frame 0 for consistent mask caching and UX
+        if self.create_frame_slider and hasattr(self, "frame_slider"):
+            self.frame_slider.blockSignals(True)
+            self.frame_slider.setValue(0)
+            self.frame_slider.blockSignals(False)
+            self.change_frame(0)
+        elif self.stack_length > 0:
+            self.change_frame(0)
+
         if self.thresh is not None:
             self.compute_mask(self.thresh)
 
@@ -138,8 +145,8 @@ class ThresholdedStackVisualizer(StackVisualizer):
             slider_range=(self.thresh_min, np.amax([self.thresh_max, init_value])),
             decimal_option=True,
             precision=4,
+            layout_ratio=(0.15, 0.85),
         )
-        thresh_layout.setContentsMargins(15, 0, 15, 0)
         self.threshold_slider.valueChanged.connect(self.change_threshold)
         if self.show_threshold_slider:
             self.canvas.layout.addLayout(thresh_layout)
@@ -154,8 +161,8 @@ class ThresholdedStackVisualizer(StackVisualizer):
             slider_range=(0, 1),
             decimal_option=True,
             precision=3,
+            layout_ratio=(0.15, 0.85),
         )
-        opacity_layout.setContentsMargins(15, 0, 15, 0)
         self.opacity_slider.valueChanged.connect(self.change_mask_opacity)
         if self.show_opacity_slider:
             self.canvas.layout.addLayout(opacity_layout)
@@ -190,7 +197,8 @@ class ThresholdedStackVisualizer(StackVisualizer):
         if self.thresh is not None:
             self.compute_mask(self.thresh)
             mask = np.ma.masked_where(self.mask == 0, self.mask)
-            self.im_mask.set_data(mask)
+            if hasattr(self, "im_mask"):
+                self.im_mask.set_data(mask)
             self.canvas.canvas.draw_idle()
 
     def change_frame(self, value):
@@ -219,7 +227,7 @@ class ThresholdedStackVisualizer(StackVisualizer):
             threshold_image,
         )
 
-        edge = estimate_unreliable_edge(self.preprocessing)
+        edge = estimate_unreliable_edge(self.preprocessing or [])
 
         if isinstance(threshold_value, (list, np.ndarray, tuple)):
             self.mask = threshold_image(

celldetective/utils/cellpose_utils/__init__.py

@@ -104,14 +104,27 @@ def _prep_cellpose_model(
       `diam_labels` are attributes of the model.
     """
 
-    import torch
+    try:
+        import torch
+    except ImportError as e:
+        raise RuntimeError(
+            "Torch is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[process]\n"
+        ) from e
 
     if not use_gpu:
         device = torch.device("cpu")
     else:
         device = torch.device("cuda")
 
-    from cellpose.models import CellposeModel
+    try:
+        from cellpose.models import CellposeModel
+    except ImportError as e:
+        raise RuntimeError(
+            "Cellpose is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[process]\n"
+            "Or specifically: pip install celldetective[cellpose]"
+        ) from e
 
     try:
         model = CellposeModel(

celldetective/utils/downloaders.py

@@ -77,18 +77,39 @@ def download_url_to_file(url, dst, progress=True):
                     Default: True
 
     """
-    file_size = None
     import ssl
+    import time
+    from urllib.error import HTTPError, URLError
 
+    file_size = None
     ssl._create_default_https_context = ssl._create_unverified_context
-    u = urlopen(url)
-    meta = u.info()
-    if hasattr(meta, "getheaders"):
-        content_length = meta.getheaders("Content-Length")
-    else:
-        content_length = meta.get_all("Content-Length")
-    if content_length is not None and len(content_length) > 0:
-        file_size = int(content_length[0])
+
+    # Retry configuration
+    max_retries = 5
+    retry_delay = 10  # Initial delay in seconds
+
+    for attempt in range(max_retries):
+        try:
+            u = urlopen(url)
+            meta = u.info()
+            if hasattr(meta, "getheaders"):
+                content_length = meta.getheaders("Content-Length")
+            else:
+                content_length = meta.get_all("Content-Length")
+            if content_length is not None and len(content_length) > 0:
+                file_size = int(content_length[0])
+            break  # Success
+        except (HTTPError, URLError) as e:
+            if attempt < max_retries - 1:
+                logger.warning(
+                    f"Download check failed: {e}. Retrying in {retry_delay}s..."
+                )
+                time.sleep(retry_delay)
+                retry_delay *= 2  # Exponential backoff
+            else:
+                logger.error(f"Download check failed after {max_retries} attempts: {e}")
+                raise e
+
     # We deliberately save it in a temp file and move it after
     dst = os.path.expanduser(dst)
     dst_dir = os.path.dirname(dst)
@@ -143,14 +164,27 @@ def download_url_to_file(url, dst, progress=True):
                 unit_divisor=1024,
             ) as pbar:
                 while True:
-                    buffer = u.read(8192)  # 8192
-                    if len(buffer) == 0:
-                        break
-                    f.write(buffer)
-                    pbar.update(len(buffer))
+                    try:
+                        buffer = u.read(8192)  # 8192
+                        if len(buffer) == 0:
+                            break
+                        f.write(buffer)
+                        pbar.update(len(buffer))
+                    except (HTTPError, URLError) as e:
+                        # Attempt rudimentary resume-like behavior or just fail?
+                        # Simple retry of read is hard without Range headers on a stream.
+                        # Best to just fail the whole download and rely on outer retry if we wrapped the whole thing.
+                        # For now, let's just let it raise, but really we should wrap the whole download block.
+                        raise e
 
         f.close()
         shutil.move(f.name, dst)
+    except Exception as e:
+        f.close()
+        remove_file_if_exists(f.name)
+        # If we failed during download reading (after open), we should probably retry the whole function from start
+        # but that requires significant refactoring. Given the error was 504 on open, the retry block above handles it.
+        raise e
     finally:
         f.close()
         remove_file_if_exists(f.name)

celldetective/utils/stardist_utils/__init__.py

@@ -43,7 +43,14 @@ def _prep_stardist_model(
     - GPU support depends on the availability of compatible hardware and software setup.
     """
 
-    from stardist.models import StarDist2D
+    try:
+        from stardist.models import StarDist2D
+    except ImportError as e:
+        raise RuntimeError(
+            "StarDist is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[process]\n"
+            "Or specifically: pip install celldetective[stardist]"
+        ) from e
 
     model = StarDist2D(None, name=model_name, basedir=path)
     model.config.use_gpu = use_gpu

{celldetective-1.5.0b4.dist-info → celldetective-1.5.0b6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b4
+Version: 1.5.0b6
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -15,11 +15,8 @@ Requires-Dist: sphinx_rtd_theme
 Requires-Dist: sphinx
 Requires-Dist: jinja2
 Requires-Dist: ipykernel
-Requires-Dist: stardist
-Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari<0.6.0
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -48,6 +45,19 @@ Requires-Dist: prettyprint
 Requires-Dist: pandas
 Requires-Dist: matplotlib
 Requires-Dist: prettytable
+Requires-Dist: scikit-image
+Requires-Dist: natsort
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow~=2.15.0; extra == "tensorflow"
+Requires-Dist: stardist; extra == "tensorflow"
+Provides-Extra: process
+Requires-Dist: cellpose<3; extra == "process"
+Requires-Dist: stardist; extra == "process"
+Requires-Dist: tensorflow~=2.15.0; extra == "process"
+Provides-Extra: all
+Requires-Dist: cellpose<3; extra == "all"
+Requires-Dist: stardist; extra == "all"
+Requires-Dist: tensorflow~=2.15.0; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
@@ -55,6 +65,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
 Dynamic: license-file
+Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: summary
 
@@ -148,10 +159,12 @@ To use the software, you must install python, *e.g.* through
 
 Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
 
-With the proper Python version, Celldetective can be directly installed with `pip`:
+With the proper Python version, Celldetective can be directly installed with `pip`.
+**Important**: By default, `pip install celldetective` will **not** install deep-learning libraries (`tensorflow`, `cellpose`, `stardist`) to allow users to manage their own GPU environment (e.g. `torch`, `cuda`).
 
+If you want the standard full installation (recommended for most users), use:
 ``` bash
-pip install celldetective
+pip install celldetective[all]
 ```
 
 We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
@@ -160,7 +173,7 @@ with `conda`:
 ``` bash
 conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
-pip install celldetective
+pip install celldetective[all]
 ```
 
 Need an update? Simply type the following in the terminal (in your

{celldetective-1.5.0b4.dist-info → celldetective-1.5.0b6.dist-info}/RECORD

@@ -1,6 +1,6 @@
 celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
 celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
-celldetective/_version.py,sha256=i0XQAcqdHCcwV-JF_A_FeVVfTjXROj_WnqM2Ktzzq1Q,24
+celldetective/_version.py,sha256=2t7jfGYhecNEZFNHUmz-D7GUPyvfrkDim4ynpi-TYII,24
 celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
 celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
 celldetective/extra_properties.py,sha256=s_2R4_El2p-gQNZ_EpgDxgrN3UnRitN7KDKHhyLuoHc,21681
@@ -45,7 +45,7 @@ celldetective/gui/base/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 celldetective/gui/base/channel_norm_generator.py,sha256=JqNAo87zA3nMKzkGjvoeV-SHI89eIATwQj4jHv3-LpI,13973
 celldetective/gui/base/components.py,sha256=jNUsCU_QE7QUFR0_xEvEPFEBYolMJt7YXGUKMjF7uOE,8155
 celldetective/gui/base/feature_choice.py,sha256=n1T2fPoNLiTDS_6fa_GuGReDhBW11HdUrKy2RywotF8,2800
-celldetective/gui/base/figure_canvas.py,sha256=dQlmLfB3PUttFmyHZIvSc_9GQ5JRy7jH9w7lyKAGElk,1523
+celldetective/gui/base/figure_canvas.py,sha256=DAAGQAcoR6yubFSsRNRZcpxgdYOWgEHtJqWhv_G7lj0,2195
 celldetective/gui/base/list_widget.py,sha256=_WU3ZRU7UcJZIxm8qx_5HF7IK7dUu8IU1FY2AaW_qgo,4694
 celldetective/gui/base/styles.py,sha256=3Kz1eXw6OLr90wtErhK0KPJyJbyhAlqkniqm0JNGwFc,7407
 celldetective/gui/base/utils.py,sha256=KojauRKGM9XKNhaWn211p6mJNZWIHLH75yeLpDd7pvA,1103
@@ -87,12 +87,12 @@ celldetective/gui/table_ops/_merge_one_hot.py,sha256=gKRgem-u_-JENkVkbjRobsH4TkS
 celldetective/gui/table_ops/_query_table.py,sha256=K-XHSZ1I4v2wwqWjyQAgyFRZJbem3CmTfHmO0vijh9g,1345
 celldetective/gui/table_ops/_rename_col.py,sha256=UAgDSpXJo_h4pLJpHaNc2w2VhbaW4D2JZTgJ3cYC4-g,1457
 celldetective/gui/viewers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/gui/viewers/base_viewer.py,sha256=gHe9QBX6Lrn567Kc-9T6KoGuLqEP_1q4RROFBd9qLWE,29962
-celldetective/gui/viewers/channel_offset_viewer.py,sha256=aQpxrJX9qM_xX848XnFrxrhTqE22DIshtD-uKL8e4gU,12423
+celldetective/gui/viewers/base_viewer.py,sha256=wA2Zrje5nQSUmwnAFCe9hcL1MOWg8uMKwFTWhEYiMXI,32159
+celldetective/gui/viewers/channel_offset_viewer.py,sha256=cywBkxyMPyKIuwZTGA03DBSS4a-H1SAohMJYOPISLEE,16289
 celldetective/gui/viewers/contour_viewer.py,sha256=riHj03LKXLoa-Ys2o2EhCE5nULfcHMohx9LFoXbI6zU,14720
 celldetective/gui/viewers/size_viewer.py,sha256=uXITjaxg5dhQ09Q6TNUxwLxi-ZglyGFcxEH1RtGIZWw,6020
 celldetective/gui/viewers/spot_detection_viewer.py,sha256=JO7kcqATHXR91lLvo8aQ5xVYdtxkMxV-xx36s01VlNQ,12545
-celldetective/gui/viewers/threshold_viewer.py,sha256=CBc6Y7cGK5U3ptAMMkmRLBvm5yl7pjGEUJjB4PKWjfM,11627
+celldetective/gui/viewers/threshold_viewer.py,sha256=F-13JF2wFhyvvKfUvgRcSjWL3leAliOXy5yUergndnE,12000
 celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
 celldetective/icons/logo.png,sha256=wV2OS8_dU5Td5cgdPbCOU3JpMpTwNuYLnfVcnQX0tJA,2437
 celldetective/icons/signals_icon.png,sha256=vEiKoqWTtN0-uJgVqtAlwCuP-f4QeWYOlO3sdp2tg2w,3969
@@ -143,7 +143,7 @@ celldetective/utils/color_mappings.py,sha256=yarqOTSrTsnOPPiPrrN_vLoPCbgWqF3wjqF
 celldetective/utils/data_cleaning.py,sha256=K-2gScxLreX7QkrM0h3dZdP0IsmvCzcxNh2-M9PALZY,22025
 celldetective/utils/data_loaders.py,sha256=6Jg99U93qYjjs2xZErc2cz37tcH5e4vEqDH8PJgoEJs,17077
 celldetective/utils/dataset_helpers.py,sha256=3ezpHO6nytw2Mx0D3maP_4535V2ohOTQn6Qpfk8gnms,6898
-celldetective/utils/downloaders.py,sha256=BIl_8XCeaKvtMVC36WITT2g5-O-n0csoMEQXVoa1B4o,7887
+celldetective/utils/downloaders.py,sha256=o5sogEeYr-LR8mp1D7uNHH1aUJN3V82VVwYZvoSNTkQ,9506
 celldetective/utils/experiment.py,sha256=bgADS70QuW4KGbzDJbVpVM-tw4qmZKMWtDT1cSxugrY,58342
 celldetective/utils/image_augmenters.py,sha256=USYd8z6dVn5z1x96IYJ4mG0smN9I_S21QMGU0wyHmjc,11654
 celldetective/utils/image_cleaning.py,sha256=KliQ3K5hdwPx4eFxJnmg3yi-ZIoimEveunPJkbbA6wA,2388
@@ -161,12 +161,12 @@ celldetective/utils/parsing.py,sha256=1zpIH9tyULCRmO5Kwzy6yA01fqm5uE_mZKYtondy-V
 celldetective/utils/resources.py,sha256=3Fz_W0NYWl_Ixc2AjEmkOv5f7ejXerCLJ2z1iWhGWUI,1153
 celldetective/utils/stats.py,sha256=4TVHRqi38Y0sed-izaMI51sMP0fd5tC5M68EYyfJjkE,3636
 celldetective/utils/types.py,sha256=lRfWSMVzTkxgoctGGp0NqD551akuxu0ygna7zVGonTg,397
-celldetective/utils/cellpose_utils/__init__.py,sha256=MeRDojrAkBSXe-wlLu5KIih5wXP9B2aPdP39JLYpoGE,5417
+celldetective/utils/cellpose_utils/__init__.py,sha256=XUG6T9RFwJ2H2jrz9eO58gYHjI6vxMe93ZeDD35DChg,5999
 celldetective/utils/event_detection/__init__.py,sha256=KX20PwPTevdbZ-25otDy_QTmealcDx5xNCfH2SOVIZM,323
 celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
-celldetective/utils/stardist_utils/__init__.py,sha256=e9s3DEaTKCUOGZb5k_DgShBTl4B0U-Jmg3Ioo8D5PyE,3978
-celldetective-1.5.0b4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective/utils/stardist_utils/__init__.py,sha256=eQiZz7UQbwkFS6zXOJFofoNm2wE7ylt-7hdCOd9uOWc,4304
+celldetective-1.5.0b6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_cellpose_fallback.py,sha256=BJZTDFF8sFR1x7rDbvZQ2RQOB1OP6wuFBRfc8zbl5zw,3513
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
@@ -175,6 +175,7 @@ tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
 tests/test_measure.py,sha256=FEUAs1rVHylvIvubCb0bJDNGZLVmkgXNgI3NaGQ1dA8,4542
 tests/test_neighborhood.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
 tests/test_notebooks.py,sha256=7HVmYiytsz0QIJ11iRkGGs4_hzNjofXAUs_OZou3Gm0,301
+tests/test_partial_install.py,sha256=G69-GNcJ9YNgs6K2bVTEZO0Jpb14xMRQWTm8A6VuIco,2841
 tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
 tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
 tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
@@ -185,8 +186,8 @@ tests/gui/test_enhancements.py,sha256=3x9au_rkQtMZ94DRj3OaEHKPr511RrWqBAUAcNQn1y
 tests/gui/test_measure_annotator_bugfix.py,sha256=tPfgWNKC0UkvrVssSrUcVDC1qgpzx6l2yCqvKtKYkM4,4544
 tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
 tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
-celldetective-1.5.0b4.dist-info/METADATA,sha256=VgzQFDS1ExiiQdY4MjqmWfrRTC-MJQR1meL7t0Q8eMY,10947
-celldetective-1.5.0b4.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-celldetective-1.5.0b4.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.5.0b4.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.5.0b4.dist-info/RECORD,,
+celldetective-1.5.0b6.dist-info/METADATA,sha256=7e7KJTEzTLZx7T0o4ITML6CI6PM8EwXU4ENpB0uymNc,11691
+celldetective-1.5.0b6.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+celldetective-1.5.0b6.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.5.0b6.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.5.0b6.dist-info/RECORD,,

{celldetective-1.5.0b4.dist-info → celldetective-1.5.0b6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.10.1)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tests/test_partial_install.py

@@ -0,0 +1,75 @@
+import unittest
+from unittest.mock import MagicMock, patch
+import sys
+import importlib
+
+
+class TestPartialValidation(unittest.TestCase):
+
+    def test_imports_without_extras(self):
+        """Test that main modules can be imported even if optional extras are missing."""
+        # This test assumes the environment MIGHT have them, so we must mock them as missing
+        # to ensure the code handles it.
+
+        with patch.dict(
+            sys.modules,
+            {
+                "tensorflow": None,
+                "torch": None,
+                "stardist": None,
+                "cellpose": None,
+                "cellpose.models": None,
+                "stardist.models": None,
+            },
+        ):
+            # Force reload of celldetective.segmentation to test its imports
+            try:
+                import celldetective.segmentation
+
+                importlib.reload(celldetective.segmentation)
+            except ImportError as e:
+                self.fail(
+                    f"Could not import celldetective.segmentation without extras: {e}"
+                )
+            except Exception as e:
+                self.fail(f"Unexpected error importing celldetective.segmentation: {e}")
+
+    def test_graceful_failure_stardist(self):
+        """Test that calling stardist functions raises RuntimeError if missing."""
+        with patch.dict(sys.modules, {"stardist": None, "stardist.models": None}):
+            # We need to reload the util module to pick up the missing module
+            import celldetective.utils.stardist_utils
+
+            importlib.reload(celldetective.utils.stardist_utils)
+
+            from celldetective.utils.stardist_utils import _prep_stardist_model
+
+            with self.assertRaises(RuntimeError) as cm:
+                _prep_stardist_model("fake_model", "fake_path")
+
+            self.assertIn("StarDist is not installed", str(cm.exception))
+
+    def test_graceful_failure_cellpose(self):
+        """Test that calling cellpose functions raises RuntimeError if missing."""
+        with patch.dict(
+            sys.modules, {"cellpose": None, "cellpose.models": None, "torch": None}
+        ):
+            import celldetective.utils.cellpose_utils
+
+            importlib.reload(celldetective.utils.cellpose_utils)
+
+            from celldetective.utils.cellpose_utils import _prep_cellpose_model
+
+            with self.assertRaises(RuntimeError) as cm:
+                _prep_cellpose_model("fake_model", "fake_path")
+
+            # Message check might correspond to torch or cellpose depending on which import hits first
+            # Our code checks torch first.
+            self.assertTrue(
+                "Torch is not installed" in str(cm.exception)
+                or "Cellpose is not installed" in str(cm.exception)
+            )
+
+
+if __name__ == "__main__":
+    unittest.main()