spacr 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

spacr/core.py

@@ -417,8 +417,8 @@ def generate_cellpose_masks(src, settings, object_type):
                 else:
                     mask_stack = _masks_to_masks_stack(masks)
 
-                    if settings['plot']:
-                        plot_cellpose4_output(batch_list, masks, flows, cmap='inferno', figuresize=figuresize, nr=1, print_object_number=True)
+                    #if settings['plot']:
+                    #    plot_cellpose4_output(batch_list, masks, flows, cmap='inferno', figuresize=figuresize, nr=1, print_object_number=True)
         
             if not np.any(mask_stack):
                 avg_num_objects_per_image, average_obj_size = 0, 0

spacr/gui_core.py

@@ -176,7 +176,6 @@ def display_figure(fig):
             show_next_figure()
             
     def zoom(event):
-        # Define zoom factors
         zoom_in_factor = 1 / 1.2
         zoom_out_factor = 1.2
 
@@ -187,83 +186,49 @@ def display_figure(fig):
         else:
             return
 
+        # Find the axis under the cursor
+        ref_ax = None
         for ax in canvas.figure.get_axes():
-            # Convert canvas pixel (event.x, event.y) to axis data coordinates
-            # EVEN IF the mouse is over a different axis, we use the same pixel to data mapping for each
-            inv = ax.transData.inverted()
-            try:
-                data_x, data_y = inv.transform((event.x, event.y))
-            except ValueError:
-                continue  # e.g. axis has no data
-
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-
-            # Zoom around (data_x, data_y) in *that axis's* data space
-            new_xlim = [data_x - (data_x - xlim[0]) * factor,
-                        data_x + (xlim[1] - data_x) * factor]
-            new_ylim = [data_y - (data_y - ylim[0]) * factor,
-                        data_y + (ylim[1] - data_y) * factor]
-
-            ax.set_xlim(new_xlim)
-            ax.set_ylim(new_ylim)
-
-            # Clip text labels
-            for label in ax.texts:
-                label.set_clip_on(True)
-
-            # Update label visibility
-            if hasattr(ax, '_label_annotations'):
-                for label in ax._label_annotations:
-                    x, y = label.get_position()
-                    is_visible = (new_xlim[0] <= x <= new_xlim[1]) and (new_ylim[0] <= y <= new_ylim[1])
-                    label.set_visible(is_visible)
-
-        canvas.draw_idle()
+            if ax.get_window_extent().contains(event.x, event.y):
+                ref_ax = ax
+                break
 
-    def zoom_v2(event):
-        # Define zoom factors
-        zoom_in_factor = 1 / 1.2
-        zoom_out_factor = 1.2
+        if ref_ax is None:
+            return
 
-        if event.num == 4 or (hasattr(event, 'delta') and event.delta > 0):
-            factor = zoom_in_factor
-        elif event.num == 5 or (hasattr(event, 'delta') and event.delta < 0):
-            factor = zoom_out_factor
-        else:
+        try:
+            # Convert mouse position to data coords in reference axis
+            data_x, data_y = ref_ax.transData.inverted().transform((event.x, event.y))
+        except ValueError:
             return
 
+        # Get current limits
+        xlim = ref_ax.get_xlim()
+        ylim = ref_ax.get_ylim()
+
+        # Compute new limits for the reference axis
+        new_xlim = [
+            data_x - (data_x - xlim[0]) * factor,
+            data_x + (xlim[1] - data_x) * factor
+        ]
+        new_ylim = [
+            data_y - (data_y - ylim[0]) * factor,
+            data_y + (ylim[1] - data_y) * factor
+        ]
+
+        # Apply the same limits to all axes
         for ax in canvas.figure.get_axes():
-            # Translate mouse position to figure coordinates
-            mouse_x, mouse_y = event.x, event.y
-            inv = ax.transData.inverted()
-            data_x, data_y = inv.transform((mouse_x, mouse_y))
-
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-
-            # Compute new limits centered on the mouse data position
-            new_width = (xlim[1] - xlim[0]) * factor
-            new_height = (ylim[1] - ylim[0]) * factor
-
-            new_xlim = [data_x - (data_x - xlim[0]) * factor,
-                        data_x + (xlim[1] - data_x) * factor]
-            new_ylim = [data_y - (data_y - ylim[0]) * factor,
-                        data_y + (ylim[1] - data_y) * factor]
-
             ax.set_xlim(new_xlim)
             ax.set_ylim(new_ylim)
 
-            # Clip all text labels to the axes area
             for label in ax.texts:
                 label.set_clip_on(True)
 
-            # Update label visibility based on new limits
             if hasattr(ax, '_label_annotations'):
                 for label in ax._label_annotations:
                     x, y = label.get_position()
-                    is_visible = (new_xlim[0] <= x <= new_xlim[1]) and (new_ylim[0] <= y <= new_ylim[1])
-                    label.set_visible(is_visible)
+                    visible = new_xlim[0] <= x <= new_xlim[1] and new_ylim[0] <= y <= new_ylim[1]
+                    label.set_visible(visible)
 
         canvas.draw_idle()
         

spacr/gui_utils.py

@@ -242,45 +242,9 @@ def annotate(settings):
                       threshold=settings['threshold'],
                       normalize_channels=settings['normalize_channels'])
     
-    #next_button = tk.Button(root, text="Next", command=app.next_page)
-    #next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
-    #back_button = tk.Button(root, text="Back", command=app.previous_page)
-    #back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
-    #exit_button = tk.Button(root, text="Exit", command=app.shutdown)
-    #exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
-    
     app.load_images()
     root.mainloop()
 
-def generate_annotate_fields_v1(frame):
-    from .settings import set_annotate_default_settings
-    from .gui_elements import set_dark_style
-
-    style_out = set_dark_style(ttk.Style())
-    font_loader = style_out['font_loader']
-    font_size = style_out['font_size'] - 2
-
-    vars_dict = {}
-    settings = set_annotate_default_settings(settings={})
-    
-    for setting in settings:
-        vars_dict[setting] = {
-            'entry': ttk.Entry(frame),
-            'value': settings[setting]
-        }
-
-    # Arrange input fields and labels
-    for row, (name, data) in enumerate(vars_dict.items()):
-        tk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:", bg=style_out['bg_color'], fg=style_out['fg_color'], font=font_loader.get_font(size=font_size)).grid(row=row, column=0)
-        if isinstance(data['value'], list):
-            # Convert lists to comma-separated strings
-            data['entry'].insert(0, ','.join(map(str, data['value'])))
-        else:
-            data['entry'].insert(0, data['value'])
-        data['entry'].grid(row=row, column=1)
-    
-    return vars_dict
-
 def generate_annotate_fields(frame):
     from .settings import set_annotate_default_settings
     from .gui_elements import set_dark_style
@@ -496,8 +460,6 @@ def function_gui_wrapper(function=None, settings={}, q=None, fig_queue=None, imp
         # Restore the original plt.show function
         plt.show = original_show
         
-
-                    
 def run_function_gui(settings_type, settings, q, fig_queue, stop_requested):
     
     from .core import generate_image_umap, preprocess_generate_masks

{spacr-1.0.0.dist-info → spacr-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 1.0.0
+Version: 1.0.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -91,12 +91,15 @@ Requires-Dist: opencv-python-headless ; extra == 'headless'
    :target: https://github.com/EinarOlafsson/spacr/blob/main/LICENSE
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -123,7 +126,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -141,8 +143,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -201,7 +202,7 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
 
 License
 -------
@@ -213,3 +214,10 @@ How to Cite
 If you use spaCR in your research, please cite:  
 Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

{spacr-1.0.0.dist-info → spacr-1.0.1.dist-info}/RECORD

@@ -8,12 +8,12 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
-spacr/core.py,sha256=SDsJsgarbMHDw2i4OOMCKtMtVx9t1tjsGCVs6iHPj7s,46638
+spacr/core.py,sha256=A1PCJHtlYjJBMdIY0QH1VcrmjsAZy-JYVHQcBXQ5za8,46640
 spacr/deep_spacr.py,sha256=055tIo3WP3elGFiIuSZaLURgu2XyUDxAdbw5ezASEqM,54526
 spacr/gui.py,sha256=NhMh96KoArrSAaJBV6PhDQpIC1cQpxgb6SclhRbYG8s,8122
-spacr/gui_core.py,sha256=pXTswrqPMTb2mgF_mvnCzBgmXEaf9w7wDnSD6uMA67w,56228
+spacr/gui_core.py,sha256=kgOXpQiBp4QXp08KViWinDVB6pVM7Gfn26bKeees6tM,54561
 spacr/gui_elements.py,sha256=OTU7aeLrPiMUTnyCT-J7ygng3beI9tdA0MmypOavEkw,156123
-spacr/gui_utils.py,sha256=F6KfNY3OqNkvfkOP1rxwBha5IOdLVyBgqZYPw3xPLes,42293
+spacr/gui_utils.py,sha256=1mWns46yK-CQpbhtERSTPx7KXBYPUIQz2UnFFxNxOrU,40749
 spacr/io.py,sha256=g6vybQeGLdTXrAqEjM6X1aoB6lyZVUq6pTI0ASppX4g,159257
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=nYvrfVfCIqD1AUk4QBE2jtpeSFtLdfUcnkhkqf9G4xQ,60877
@@ -103,9 +103,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-1.0.0.dist-info/LICENSE,sha256=t0Pov6pnK8thLteoF4xZGmdCwe5mhNwl3OXxLYTGD9U,1081
-spacr-1.0.0.dist-info/METADATA,sha256=FAPU_0wMd3rz1-fbRo0TS568-_O7_NIWgx1jXPM4fuE,10356
-spacr-1.0.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-spacr-1.0.0.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-1.0.0.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-1.0.0.dist-info/RECORD,,
+spacr-1.0.1.dist-info/LICENSE,sha256=t0Pov6pnK8thLteoF4xZGmdCwe5mhNwl3OXxLYTGD9U,1081
+spacr-1.0.1.dist-info/METADATA,sha256=C_PPoW7NPT7RH3d3iJ2yfX3GR8cy-uQ8tx1RGmqq854,10963
+spacr-1.0.1.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+spacr-1.0.1.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-1.0.1.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-1.0.1.dist-info/RECORD,,