flimkit 0.13.0__tar.gz → 0.13.2__tar.gz

{flimkit-0.13.0 → flimkit-0.13.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flimkit
-Version: 0.13.0
+Version: 0.13.2
 Summary: Fluorescence lifetime imaging analysis: reading, fitting, phasors and stitching
 Author-email: Alex Hunt <alexander.hunt@ed.ac.uk>
 License-Expression: MIT
@@ -39,13 +39,16 @@ Requires-Dist: tifffile
 Requires-Dist: tqdm==4.67.3
 Requires-Dist: xarray==2026.1.0
 Provides-Extra: gui
-Requires-Dist: tkinterdnd2==0.4.3; extra == "gui"
+Requires-Dist: tkinterdnd2>=0.6.2; extra == "gui"
 Requires-Dist: TKinterModernThemes; extra == "gui"
+Requires-Dist: sv-ttk>=2.6.1; extra == "gui"
 Provides-Extra: notebook
 Requires-Dist: ipython==9.10.0; extra == "notebook"
 Requires-Dist: ipywidgets==8.1.8; extra == "notebook"
 Provides-Extra: segmentation
 Requires-Dist: cellpose>=3.0; extra == "segmentation"
+Provides-Extra: cellpose
+Requires-Dist: flimkit[segmentation]; extra == "cellpose"
 Provides-Extra: mlx
 Requires-Dist: mlx; extra == "mlx"
 Provides-Extra: torch

{flimkit-0.13.0 → flimkit-0.13.2}/flimkit/UI/gui.py

@@ -3886,7 +3886,6 @@ if HAS_TKMT:
             self.root.minsize(760, 700)
             self._init_ui()
             self._run_plugin_startups()
-            self.run(cleanresize=False)
 
 class FLIMKitGUIFallback(_UIBuilder):
     def __init__(self, root):
@@ -3895,7 +3894,41 @@ class FLIMKitGUIFallback(_UIBuilder):
         self.root.minsize(760, 700)
         self._init_ui()
         self._run_plugin_startups()
-        self.root.mainloop()
+
+def discard_default_root():
+    root = getattr(tk, '_default_root', None)
+    if root is None:
+        return
+    try:
+        root.destroy()
+    except Exception:
+        pass
+    tk._default_root = None
+
+def plain_root():
+    if HAS_DND:
+        try:
+            from tkinterdnd2 import Tk
+            return Tk()
+        except Exception as exc:
+            print(f'Drag and drop is off, the tkdnd library would not load: {exc}')
+            discard_default_root()
+    return tk.Tk()
+
+def apply_fallback_theme(root):
+    try:
+        import sv_ttk
+        sv_ttk.set_theme('dark')
+        return 'sun-valley through sv_ttk'
+    except Exception:
+        pass
+    style = ttk.Style(root)
+    names = style.theme_names()
+    for theme_name in ('vista', 'aqua', 'clam', 'alt', 'default'):
+        if theme_name in names:
+            style.theme_use(theme_name)
+            return theme_name
+    return style.theme_use()
 
 def launch_gui():
     global GUI_MODE
@@ -3904,20 +3937,21 @@ def launch_gui():
     init_crash_handler()
     from flimkit import plugins
     plugins.ensure_loaded()
+    themed = None
     if HAS_TKMT:
-        app = FLIMKitGUIThemed(theme='sun-valley', mode='dark')
-    else:
-        if HAS_DND:
-            from tkinterdnd2 import Tk
-            root = Tk()
-        else:
-            root = tk.Tk()
-        style = ttk.Style(root)
-        for theme_name in ('clam', 'alt', 'default'):
-            if theme_name in style.theme_names():
-                style.theme_use(theme_name)
-                break
-        app = FLIMKitGUIFallback(root)
+        try:
+            themed = FLIMKitGUIThemed(theme='sun-valley', mode='dark')
+        except tk.TclError as exc:
+            discard_default_root()
+            print(f'The themed window would not start on this Tk: {exc}')
+            print('Falling back. Tk 9 needs tkinterdnd2 0.6.2 or newer and sv-ttk.')
+    if themed is not None:
+        themed.run(cleanresize=False)
+        return
+    root = plain_root()
+    print(f'Theme: {apply_fallback_theme(root)}')
+    FLIMKitGUIFallback(root)
+    root.mainloop()
 
 if __name__ == '__main__':
     launch_gui()

{flimkit-0.13.0 → flimkit-0.13.2}/flimkit/_version.py

@@ -1,4 +1,4 @@
-__version__ = '0.13.0'
+__version__ = '0.13.2'
 fitter_version = '20'
 
 roadmap = '''Flim program roadmap:
@@ -39,5 +39,7 @@ Need to add Phasor once added to the codebase, and update version to 1.0. And ad
 0.11.0 -> a bridge to QuPath: FLIMKit serves its intensity and lifetime images and its ROIs over a loopback HTTP connection, so QuPath reads and writes them directly instead of going through exported files, against the image already open in a live session, and can put the FLIMKit images into the open project beside a brightfield image. Plugins gain two hooks: @startup(id, order) runs a callback once the window is built, for an add-on that has to be doing something from launch, and @panel_button(id, label, panel, order) puts a button in the ROI panel's action grid. A startup that raises is reported and the rest still run. Freehand ROIs whose outline crosses itself no longer export as self-intersecting GeoJSON, which RFC 7946 does not allow and which made QuPath reject a whole FeatureCollection over one bad region; such a ring is repaired to its outer boundary and carries repaired: self-intersecting. Three of five hand-drawn regions in a real session were affected. Adds shapely as a dependency.
 0.12.0 -> on PyPI, so pip install flimkit gets the analysis core without the desktop, with gui, torch, mlx, notebook, segmentation and test as extras. Plugins now load when a format is looked up, so a plugin-registered format works from a script or a CLI and not only from the GUI. Per-pixel fitting on the GPU works in pixel blocks, so a field larger than a gigabyte reaches the GPU instead of silently falling back to the CPU; a 1024 square field fits in 7.8s against 25.2s on the CPU. The per-pixel tau grid goes from 200 points to 1600, which cuts the error against known-truth synthetic data from 0.021 ns to 0.008 ns, so per-pixel lifetimes will differ slightly from earlier versions. Cancelling a tile fit is honoured through canvas assembly and saving rather than only during the fitting. Leica .xlef projects are read for tile positions.
 0.13.0 -> per-pixel fitting numbers move, so fitter_version goes to 20. Free-tau per-pixel fits carry their lifetimes in nanoseconds rather than seconds, which roughly halves the error against known truth and makes the CPU, CUDA and Metal paths agree to every digit reported. Pile-up correction was silently discarded on the free-tau path and now runs, and pile-up can instead go in the per-pixel forward model with --pileup-in-model, which leaves the data Poisson. The background can be fitted as a term in the model rather than subtracted, with --bg-in-model, off by default because the two routes are biased in opposite directions rather than one being better. Per-pixel chi-squared is computed in float32, which takes a 512 square fit from 2.02s to 1.50s and the test suite from 280s to 155s. The GPU block budget is per backend, 32 MB on CUDA and ROCm against 256 MB on MLX, worth a flat 2x on an A5000, and is clamped to half of free device memory.
+0.13.1 -> documentation fixes and two things found on a first run against QuPath on a fresh install. Stitching says how big the photon cube is, where it is going and how long the allocation took, and warns when the output drive cannot make sparse files, because exFAT writes the whole 57.2 GB before the first tile is read. flimkit[cellpose] works as well as flimkit[segmentation]. The docs name flimkit-bridge, say which QuPath pipeline writes the photon cube, document FLIMKIT_GPU_BLOCK_BYTES, and drop two claims that were no longer true: that the GPU backends cannot honour a fit window, and that free-tau per-pixel fitting uses batched Adam on the GPU. No fitted number changes, so fitter_version stays at 20.
+0.13.2 -> the desktop GUI starts on a Tk 9 interpreter. The Windows python.org build of Python 3.14 ships Tk 9.0 where the macOS build still ships 8.6, and two GUI dependencies were built for Tcl 8.6 only, so the window died before it opened with either an unloadable tkdnd library or an invalid command name set_theme, depending on what was installed. tkinterdnd2 moves to 0.6.2 or newer and sv-ttk joins the gui extra, both of which load on Tk 8.6 and Tk 9. FLIMKit also falls back to a plain window rather than dying when a theme or a Tcl package fails at run time, which it could not do before because it chose its path from whether the imports had worked and both libraries import cleanly before failing inside Tcl. No fitted number changes.
 1.0.0 -> release version with all core features implemented and tested
 1.5.0 (or 2.0) -> validation of fitting results with known fluorophores.'''

{flimkit-0.13.0 → flimkit-0.13.2}/flimkit/formats/PTU/stitch.py

@@ -1,4 +1,6 @@
 import json
+import os
+import time
 import numpy as np
 import tifffile
 from pathlib import Path
@@ -13,6 +15,20 @@ from ...utils.xml_utils import (
 )
 from .decode import get_flim_histogram_from_ptufile, create_time_axis
 
+def sparse_files_supported(directory):
+    probe = Path(directory) / '.flimkit_sparse_probe'
+    try:
+        with open(probe, 'wb') as handle:
+            handle.truncate(64 * 1024 * 1024)
+        return os.stat(probe).st_blocks * 512 < 32 * 1024 * 1024
+    except Exception:
+        return True
+    finally:
+        try:
+            probe.unlink()
+        except Exception:
+            pass
+
 def stitch_flim_tiles(
     xlif_path,
     ptu_dir,
@@ -74,16 +90,24 @@ def stitch_flim_tiles(
     else:
         canvas_width = max(t['pixel_x'] for t in tile_positions) + tile_x
         canvas_height = max(t['pixel_y'] for t in tile_positions) + tile_y
+    cube_gb = canvas_height * canvas_width * n_time_bins * 4 / 1e9
     if verbose:
         print(f"  Canvas: {canvas_height} × {canvas_width} pixels")
         print()
-        print('Allocating arrays...')
+        print(f'Allocating a {cube_gb:.1f} GB photon cube at {output_flim}')
+        if not sparse_files_supported(Path(output_flim).parent):
+            print(f'  {Path(output_flim).parent} cannot make sparse files, so all '
+                  f'{cube_gb:.1f} GB is written out before the first tile is read. '
+                  f'A drive formatted APFS, HFS+, NTFS or ext4 does this instantly')
+    allocation_started = time.time()
     intensity_canvas = np.zeros((canvas_height, canvas_width), dtype=np.float64)
     flim_canvas = np.memmap(
         str(output_flim), dtype=np.uint32, mode='w+',
         shape=(canvas_height, canvas_width, n_time_bins))
     _owner = np.full((canvas_height, canvas_width), -1,     dtype=np.int32)
     _min_dist2 = np.full((canvas_height, canvas_width), np.inf, dtype=np.float64)
+    if verbose:
+        print(f'  Allocated in {time.time() - allocation_started:.1f}s')
     _hists = []
     if verbose:
         print(f"Stitching {len(tile_positions)} tiles...")

{flimkit-0.13.0 → flimkit-0.13.2}/flimkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flimkit
-Version: 0.13.0
+Version: 0.13.2
 Summary: Fluorescence lifetime imaging analysis: reading, fitting, phasors and stitching
 Author-email: Alex Hunt <alexander.hunt@ed.ac.uk>
 License-Expression: MIT
@@ -39,13 +39,16 @@ Requires-Dist: tifffile
 Requires-Dist: tqdm==4.67.3
 Requires-Dist: xarray==2026.1.0
 Provides-Extra: gui
-Requires-Dist: tkinterdnd2==0.4.3; extra == "gui"
+Requires-Dist: tkinterdnd2>=0.6.2; extra == "gui"
 Requires-Dist: TKinterModernThemes; extra == "gui"
+Requires-Dist: sv-ttk>=2.6.1; extra == "gui"
 Provides-Extra: notebook
 Requires-Dist: ipython==9.10.0; extra == "notebook"
 Requires-Dist: ipywidgets==8.1.8; extra == "notebook"
 Provides-Extra: segmentation
 Requires-Dist: cellpose>=3.0; extra == "segmentation"
+Provides-Extra: cellpose
+Requires-Dist: flimkit[segmentation]; extra == "cellpose"
 Provides-Extra: mlx
 Requires-Dist: mlx; extra == "mlx"
 Provides-Extra: torch

{flimkit-0.13.0 → flimkit-0.13.2}/flimkit.egg-info/requires.txt

@@ -24,9 +24,13 @@ xarray==2026.1.0
 [all]
 flimkit[gui,notebook,segmentation]
 
+[cellpose]
+flimkit[segmentation]
+
 [gui]
-tkinterdnd2==0.4.3
+tkinterdnd2>=0.6.2
 TKinterModernThemes
+sv-ttk>=2.6.1
 
 [mlx]
 mlx

{flimkit-0.13.0 → flimkit-0.13.2}/pyproject.toml

@@ -49,8 +49,9 @@ dependencies = [
 
 [project.optional-dependencies]
 gui = [
-    'tkinterdnd2==0.4.3',
+    'tkinterdnd2>=0.6.2',
     'TKinterModernThemes',
+    'sv-ttk>=2.6.1',
 ]
 notebook = [
     'ipython==9.10.0',
@@ -59,6 +60,9 @@ notebook = [
 segmentation = [
     'cellpose>=3.0',
 ]
+cellpose = [
+    'flimkit[segmentation]',
+]
 mlx = [
     'mlx',
 ]