yabplot 0.1.4__tar.gz → 0.1.5__tar.gz

{yabplot-0.1.4/yabplot.egg-info → yabplot-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yabplot
-Version: 0.1.4
+Version: 0.1.5
 Summary: yet another brain plot
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -63,32 +63,41 @@ please refer to the [documentation](https://teanijarv.github.io/yabplot/) for mo
 import yabplot as yab
 import numpy as np
 
-# see available cortical atlases
-atlases = yab.get_available_resources(category='cortical')
-
-# see the region names within the aseg atlas
-regions = yab.get_atlas_regions(atlas='aseg', category='subcortical')
-
-# plot data on cortical regions
-data = np.arange(0, 1, 0.001)
-yab.plot_cortical(data=data, atlas='schaefer_1000', figsize=(600, 300),
-                  cmap='viridis', vminmax=[0, 1], style='default',
-                  views=['left_lateral', 'superior', 'right_lateral'])
-
-
-# plot values for specific subcortical regions
-data = {'Left_Amygdala': 0.8, 'Right_Hippocampus': 0.5, 
-        'Right_Thalamus': -0.5, 'Left_Putamen': -1}
-yab.plot_subcortical(data=data, atlas='aseg', figsize=(600, 450), layout=(2, 2),
-                     views=['superior', 'anterior', 'left_lateral', 'right_lateral'], 
-                     cmap='coolwarm', vminmax=[-1, 1], style='matte')
-
-# plot data on white matter bundles
-regions = yab.get_atlas_regions(atlas='xtract_tiny', category='tracts')
-data = np.arange(0, len(regions))
-yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300), 
-                views=['superior', 'anterior', 'left_lateral'], nan_color='#cccccc', 
-                bmesh_type='fsaverage', style='default', cmap='plasma')
+# check that you have the latest version
+print(yab.__version__)
+
+# see available atlases and brain meshes
+print(yab.get_available_resources())
+
+# see the region names for a specific atlas
+print(yab.get_atlas_regions(atlas='aseg', category='subcortical'))
+
+# cortical surfaces
+atlas = 'aparc'
+dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086, ...}
+dmap2 = {'L_fusiform': 0.218, 'L_supramarginal': 0.119, ...}
+yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='midthickness', views=['left_lateral', 'left_medial'],
+                  figsize=(600, 300), cmap='viridis', proc_vertices='sharp')
+yab.plot_cortical(data=dmap2, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='swm', views=['left_lateral', 'left_medial'],
+                  figsize=(1200, 600), cmap='viridis', proc_vertices='sharp')
+
+# subcortical structures
+atlas = 'aseg'
+regs = yab.get_atlas_regions(atlas=atlas, category='subcortical')
+data = np.arange(1, len(regs)+1)
+yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
+                     views=['left_lateral', 'superior', 'right_lateral'], 
+                     bmesh_alpha=0.1, figsize=(600, 300), cmap='viridis')
+
+# white matter bundles
+atlas = 'xtract_tiny'
+regs = yab.get_atlas_regions(atlas=atlas, category='tracts')
+data = {reg: np.sin(i) for i, reg in enumerate(regs)}
+yab.plot_tracts(data=data, atlas=atlas, style='matte',
+                views=['left_lateral', 'anterior', 'superior'], bmesh_type='pial',
+                bmesh_alpha=0.1, figsize=(1600, 800), cmap='viridis')
 
 ```
 

{yabplot-0.1.4 → yabplot-0.1.5}/README.md

@@ -40,32 +40,41 @@ please refer to the [documentation](https://teanijarv.github.io/yabplot/) for mo
 import yabplot as yab
 import numpy as np
 
-# see available cortical atlases
-atlases = yab.get_available_resources(category='cortical')
-
-# see the region names within the aseg atlas
-regions = yab.get_atlas_regions(atlas='aseg', category='subcortical')
-
-# plot data on cortical regions
-data = np.arange(0, 1, 0.001)
-yab.plot_cortical(data=data, atlas='schaefer_1000', figsize=(600, 300),
-                  cmap='viridis', vminmax=[0, 1], style='default',
-                  views=['left_lateral', 'superior', 'right_lateral'])
-
-
-# plot values for specific subcortical regions
-data = {'Left_Amygdala': 0.8, 'Right_Hippocampus': 0.5, 
-        'Right_Thalamus': -0.5, 'Left_Putamen': -1}
-yab.plot_subcortical(data=data, atlas='aseg', figsize=(600, 450), layout=(2, 2),
-                     views=['superior', 'anterior', 'left_lateral', 'right_lateral'], 
-                     cmap='coolwarm', vminmax=[-1, 1], style='matte')
-
-# plot data on white matter bundles
-regions = yab.get_atlas_regions(atlas='xtract_tiny', category='tracts')
-data = np.arange(0, len(regions))
-yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300), 
-                views=['superior', 'anterior', 'left_lateral'], nan_color='#cccccc', 
-                bmesh_type='fsaverage', style='default', cmap='plasma')
+# check that you have the latest version
+print(yab.__version__)
+
+# see available atlases and brain meshes
+print(yab.get_available_resources())
+
+# see the region names for a specific atlas
+print(yab.get_atlas_regions(atlas='aseg', category='subcortical'))
+
+# cortical surfaces
+atlas = 'aparc'
+dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086, ...}
+dmap2 = {'L_fusiform': 0.218, 'L_supramarginal': 0.119, ...}
+yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='midthickness', views=['left_lateral', 'left_medial'],
+                  figsize=(600, 300), cmap='viridis', proc_vertices='sharp')
+yab.plot_cortical(data=dmap2, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='swm', views=['left_lateral', 'left_medial'],
+                  figsize=(1200, 600), cmap='viridis', proc_vertices='sharp')
+
+# subcortical structures
+atlas = 'aseg'
+regs = yab.get_atlas_regions(atlas=atlas, category='subcortical')
+data = np.arange(1, len(regs)+1)
+yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
+                     views=['left_lateral', 'superior', 'right_lateral'], 
+                     bmesh_alpha=0.1, figsize=(600, 300), cmap='viridis')
+
+# white matter bundles
+atlas = 'xtract_tiny'
+regs = yab.get_atlas_regions(atlas=atlas, category='tracts')
+data = {reg: np.sin(i) for i, reg in enumerate(regs)}
+yab.plot_tracts(data=data, atlas=atlas, style='matte',
+                views=['left_lateral', 'anterior', 'superior'], bmesh_type='pial',
+                bmesh_alpha=0.1, figsize=(1600, 800), cmap='viridis')
 
 ```
 

{yabplot-0.1.4 → yabplot-0.1.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "yabplot"
-version = "0.1.4"
+version = "0.1.5"
 description = "yet another brain plot"
 readme = "README.md"
 requires-python = ">=3.10"

{yabplot-0.1.4 → yabplot-0.1.5}/tests/test_smoke.py

@@ -23,16 +23,16 @@ def test_plot_cortical():
     """
     Integration test: Downloads 'aparc' and plots it.
     """
-    yab.plot_cortical(atlas='aparc', display_type='none')
+    yab.plot_cortical(atlas='aparc', display_type=None)
 
 def test_plot_subcortical():
     """
     Integration test: Downloads 'aseg' and plots it.
     """
-    yab.plot_subcortical(atlas='aseg', display_type='none')
+    yab.plot_subcortical(atlas='aseg', display_type=None)
 
 def test_plot_tracts():
     """
     Integration test: Downloads 'xtract_tiny' and plots it.
     """
-    yab.plot_tracts(atlas='xtract_tiny', display_type='none')
+    yab.plot_tracts(atlas='xtract_tiny', display_type=None)

{yabplot-0.1.4 → yabplot-0.1.5}/yabplot/data/registry.txt

@@ -17,5 +17,9 @@ tracts-xtract_large.zip sha256:e2d59e9f90b024018788af87e389f93b2fa9ac21360460196
 tracts-xtract_medium.zip sha256:f095028d3dfc0f974ebef1feffe4006b5bac1366325a784ea2301c56f583b1e7 https://osf.io/7tbjg/download
 tracts-xtract_small.zip sha256:9d3fe2c57acb87e8d13eb40a49a6c2c354dbe1a020122b693e9bf713e57cad5b https://osf.io/bmn3a/download
 tracts-xtract_tiny.zip sha256:469f9ed8ed5ceb7f8e17c9a0a92f1491d540814f832ef56441a7539532111f41 https://osf.io/a73x2/download
-bmesh-conte69.zip sha256:5ba9ffc89ae7f640590a80fc188d277b1b49a34a0bd99c0c9e5cfb52fc963cac https://osf.io/h4ugr/download
-bmesh-fsaverage.zip sha256:bccec9e3fc10ffc9d1cbdb6ad2b0ffd81c93ca0fa8d26fc530d9b4d58dfcd7a0 https://osf.io/sq7am/download
+bmesh-inflated.zip sha256:ba72f9e75f16fe767f6bbcec5c98381f6a20b2f5e2092505b4692844a1686461 https://osf.io/kfzjg/download
+bmesh-midthickness.zip sha256:ef8209853e1dac8804a60b5cde0b653ef2f6c77b6c7536f7acaa69a46dbb06c0 https://osf.io/xaktf/download
+bmesh-pial.zip sha256:5e36ba7883dd2a88485fc45c9166ed48e22db607d45655242961242b51f9f126 https://osf.io/knpg8/download
+bmesh-swm.zip sha256:1a516c070cb63557751d841d5cf75772660872b89ec749ee19c23298d77fa807 https://osf.io/hpbc9/download
+bmesh-very_inflated.zip sha256:8c33a00c718a47f0af118ce2c5804a2adf13d79be05c4665ca26582e3e8dd977 https://osf.io/xp9jr/download
+bmesh-white.zip sha256:b885ac1a4dcdf9e241a97e8d3ca59d7b1c86d8a3ebe17df512993bc5c1c0354a https://osf.io/wfc5t/download

{yabplot-0.1.4 → yabplot-0.1.5}/yabplot/plotting.py

@@ -14,7 +14,8 @@ from .data import (
 from .utils import (
     load_gii, load_gii2pv, prep_data, 
     generate_distinct_colors, parse_lut, map_values_to_surface, 
-    lines_from_streamlines, make_cortical_mesh
+    get_puzzle_pieces, apply_internal_blur, apply_dilation,
+    get_smooth_mask, lines_from_streamlines, make_cortical_mesh
 )
 
 from .scene import (
@@ -26,8 +27,8 @@ from .scene import (
 # --- plot for cortical surface ---
 
 def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, layout=None, 
-                  figsize=(1000, 600), cmap='RdYlBu_r', vminmax=[None, None], 
-                  nan_color=(1.0, 1.0, 1.0), style='default', zoom=1.2, 
+                  bmesh_type='midthickness', figsize=(1000, 600), cmap='coolwarm', vminmax=[None, None], 
+                  nan_color=(1.0, 1.0, 1.0), style='default', zoom=1.2, proc_vertices=None,
                   display_type='static', export_path=None):
     """
     Visualize data on the cortical surface using a specified atlas.
@@ -54,6 +55,9 @@ def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, lay
         or a dictionary of camera configurations. Defaults to all views.
     layout : tuple (rows, cols), optional
         Grid layout for subplots. If None, automatically calculated based on the number of views.
+    bmesh_type : str
+        Name of the background context brain mesh (e.g., 'midthickness', 'white', 'swm', etc). 
+        Default is 'midthickness'.
     figsize : tuple (width, height), optional
         Window size in pixels. Default is (1000, 600).
     cmap : str or matplotlib.colors.Colormap, optional
@@ -67,6 +71,11 @@ def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, lay
         Lighting preset ('default', 'matte', 'glossy', 'sculpted', 'flat').
     zoom : float, optional
         Camera zoom level. >1.0 zooms in, <1.0 zooms out. Default is 1.2.
+    proc_vertices : str or None, optional
+        Whether to process the vertices edges according to geometry of bmesh.
+        Set to None to not perform (default).
+        'blur': Applies simple blurring between different color vertices (low performance impact).
+        'sharp': Applies sharpening of the resolution of different color vertices (high performance impact).
     display_type : {'static', 'interactive', 'none'}, optional
         'static': Returns a static image (good for notebooks).
         'interactive': Opens an interactive viewer.
@@ -80,19 +89,18 @@ def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, lay
         The plotter instance used for rendering.
     """
 
-    # defaults
+    # atlas and categorical check
     if atlas is None and custom_atlas_path is None:
         atlas = 'aparc'
+    is_cat = (data is None)
 
     # load brain mesh
-    bmesh_path = _resolve_resource_path('conte69', 'bmesh')
-    lh_v, lh_f = load_gii(os.path.join(bmesh_path, 'conte69.lh.gii'))
-    rh_v, rh_f = load_gii(os.path.join(bmesh_path, 'conte69.rh.gii'))
+    bmesh_path = _resolve_resource_path(bmesh_type, 'bmesh')
+    lh_v, lh_f = load_gii(os.path.join(bmesh_path, f'fs_LR.32k.L.{bmesh_type}.surf.gii'))
+    rh_v, rh_f = load_gii(os.path.join(bmesh_path, f'fs_LR.32k.R.{bmesh_type}.surf.gii'))
 
-    # resolve atlas path (either download or custom directory)
+    # resolve atlas
     atlas_dir = _resolve_resource_path(atlas, 'cortical', custom_path=custom_atlas_path)
-    
-    # locate files
     check_name = None if custom_atlas_path else atlas
     csv_path, lut_path = _find_cortical_files(atlas_dir, strict_name=check_name)
 
@@ -102,28 +110,43 @@ def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, lay
 
     # map data
     all_vals = map_values_to_surface(data, tar_labels, lut_ids, lut_names)
-    lh_vals = all_vals[:len(lh_v)]
-    rh_vals = all_vals[len(lh_v):]
+    lh_vals_raw = all_vals[:len(lh_v)]
+    rh_vals_raw = all_vals[len(lh_v):]
+
+    # vertices processing
+    results = []
+    for v, f, raw in [(lh_v, lh_f, lh_vals_raw), (rh_v, rh_f, rh_vals_raw)]:
+        if proc_vertices == 'sharp':
+            # razor-sharp puzzle mode
+            base, pieces = get_puzzle_pieces(v, f, raw)
+            results.append((base, pieces))
+        else:
+            # single clipper mode (blur or none)
+            v_proc = apply_internal_blur(f, raw, iterations=3, weight=0.3) if proc_vertices == 'blur' else raw
+            dilated = apply_dilation(f, v_proc, iterations=4)
+            o_guide = get_smooth_mask(f, np.where(np.isnan(raw), 0.0, 1.0), iterations=4)
+            
+            mesh = make_cortical_mesh(v, f, dilated)
+            mesh['Slice_Mask'] = o_guide
+            data_p = mesh.clip_scalar(scalars='Slice_Mask', value=0.5, invert=False)
+            base_p = mesh.clip_scalar(scalars='Slice_Mask', value=0.5, invert=True)
+            if base_p.n_points > 0: base_p['Data'] = np.full(base_p.n_points, np.nan)
+            results.append((base_p, [data_p]))
+    (lh_base, lh_parts), (rh_base, rh_parts) = results
 
     # setup colors
-    is_categorical = (data is None)
     n_colors = 256
-    if is_categorical:
+    if is_cat:
         _lut_colors = lut_colors.copy()
-        _lut_colors[0] = nan_color
+        _lut_colors[0] = nan_color # TODO: check nancolor
         cmap = ListedColormap(_lut_colors)
         n_colors = len(_lut_colors)
         vmin, vmax = 0, max_id
     else:
-        if cmap is None: cmap = 'RdYlBu_r'
         vmin = vminmax[0] if vminmax[0] is not None else np.nanmin(all_vals)
         vmax = vminmax[1] if vminmax[1] is not None else np.nanmax(all_vals)
 
-    # create meshes
-    lh_mesh = make_cortical_mesh(lh_v, lh_f, lh_vals)
-    rh_mesh = make_cortical_mesh(rh_v, rh_f, rh_vals)
-
-    # setup plotter
+    # plotter setup
     sel_views = get_view_configs(views)
     plotter, ncols, nrows = setup_plotter(sel_views, layout, figsize, display_type)
     shading_params = get_shading_preset(style)
@@ -132,46 +155,46 @@ def plot_cortical(data=None, atlas=None, custom_atlas_path=None, views=None, lay
     for i, (name, cfg) in enumerate(sel_views.items()):
         plotter.subplot(i // ncols, i % ncols)
         
-        meshes = []
-        if cfg['side'] in ['L', 'both']: meshes.append(lh_mesh)
-        if cfg['side'] in ['R', 'both']: meshes.append(rh_mesh)
-
-        for mesh in meshes:     
+        view_bases = []
+        view_pieces = []
+        if cfg['side'] in ['L', 'both']:
+            if lh_base.n_points > 0: view_bases.append(lh_base)
+            view_pieces.extend(lh_parts)
+        if cfg['side'] in ['R', 'both']:
+            if rh_base.n_points > 0: view_bases.append(rh_base)
+            view_pieces.extend(rh_parts)
+
+        # brain meshes
+        for b_mesh in view_bases:     
+            plotter.add_mesh(b_mesh, color=nan_color, smooth_shading=True, **shading_params)
+
+        # data vertices
+        for p_mesh in view_pieces:
+            if p_mesh.n_points == 0: continue
+            interp = (proc_vertices == 'blur') # only blur mode uses interpolation
+            
             actor = plotter.add_mesh(
-                mesh,
-                scalars='Data', 
-                cmap=cmap, 
-                clim=(vmin, vmax), 
-                n_colors=n_colors,
-                nan_color=nan_color, 
-                show_scalar_bar=False,
-                rgb=False, 
-                smooth_shading=True,
-                show_edges=False,
-                interpolate_before_map=False,
-                **shading_params
-            )
+                p_mesh, scalars='Data', cmap=cmap, clim=(vmin, vmax), 
+                n_colors=n_colors, nan_color=nan_color, show_scalar_bar=False,
+                smooth_shading=True, interpolate_before_map=interp, **shading_params
+            ) # rgb=False, show_edges=False, interpolate_before_map=False,
             if scalar_bar_mapper is None: scalar_bar_mapper = actor.mapper
 
         set_camera(plotter, cfg, zoom=zoom)
         plotter.hide_axes()
-
-    if not is_categorical and scalar_bar_mapper:
+        
+    if not is_cat and scalar_bar_mapper:
         plotter.subplot(nrows - 1, 0)
-        plotter.add_scalar_bar(mapper=scalar_bar_mapper, title='', n_labels=2,
-                               vertical=False, position_x=0.3, position_y=0.25, 
-                               height=0.5, width=0.4,color='black', 
-                               label_font_size=20)
+        plotter.add_scalar_bar(mapper=scalar_bar_mapper, vertical=False, position_x=0.3, position_y=0.25, height=0.5, width=0.4)
     
     return finalize_plot(plotter, export_path, display_type)
 
 
-
 # --- plot for subcortical structures ---
 
 def plot_subcortical(data=None, atlas=None, custom_atlas_path=None, views=None, layout=None, 
                      figsize=(1000, 600), cmap='coolwarm', vminmax=[None, None], nan_color='#cccccc', 
-                     nan_alpha=1.0, legend=False, style='default', bmesh_type='conte69', 
+                     nan_alpha=1.0, legend=False, style='default', bmesh_type='midthickness', 
                      bmesh_alpha=0.1, bmesh_color='lightgray', zoom=1.2, display_type='static', 
                      export_path=None, custom_atlas_proc=dict(smooth_i=15, smooth_f=0.6)):
     """
@@ -213,8 +236,8 @@ def plot_subcortical(data=None, atlas=None, custom_atlas_path=None, views=None,
     style : str, optional
         Lighting preset ('default', 'matte', 'glossy', 'sculpted', 'flat').
     bmesh_type : str or None, optional
-        Name of the background context brain mesh (e.g., 'conte69'). 
-        Set to None to hide the context brain.
+        Name of the background context brain mesh (e.g., 'midthickness', 'white', 'swm', etc). 
+        Set to None to hide the context brain. Default is 'midthickness'.
     bmesh_alpha : float, optional
         Opacity of the context brain mesh. Default is 0.1.
     bmesh_color : str, optional
@@ -246,8 +269,8 @@ def plot_subcortical(data=None, atlas=None, custom_atlas_path=None, views=None,
     bmesh = {}
     if bmesh_type:
         bmesh_path = _resolve_resource_path(bmesh_type, 'bmesh')
-        for h in ['lh', 'rh']:
-            fpath = os.path.join(bmesh_path, f'{bmesh_type}.{h}.gii')
+        for h in ['L', 'R']:
+            fpath = os.path.join(bmesh_path, f'fs_LR.32k.{h}.{bmesh_type}.surf.gii')
             if os.path.exists(fpath):
                 bmesh[h] = load_gii2pv(fpath)
     
@@ -371,7 +394,7 @@ def clear_tract_cache():
 def plot_tracts(data=None, atlas=None, custom_atlas_path=None, views=None, layout=None, 
                 figsize=(1000, 800), cmap='coolwarm', alpha=1.0, vminmax=[None, None], 
                 nan_color='#BDBDBD', nan_alpha=1.0, legend=False, style='default',
-                bmesh_type='conte69', bmesh_alpha=0.2, bmesh_color='lightgray', 
+                bmesh_type='midthickness', bmesh_alpha=0.2, bmesh_color='lightgray', 
                 zoom=1.2, orientation_coloring=False, display_type='static', 
                 tract_kwargs=dict(render_lines_as_tubes=True, line_width=1.2),
                 export_path=None):
@@ -417,8 +440,8 @@ def plot_tracts(data=None, atlas=None, custom_atlas_path=None, views=None, layou
     style : str, optional
         Lighting preset ('default', 'matte', 'glossy', 'sculpted', 'flat').
     bmesh_type : str or None, optional
-        Name of the background context brain mesh (e.g., 'conte69'). 
-        Set to None to hide the context brain.
+        Name of the background context brain mesh (e.g., 'midthickness', 'white', 'swm', etc). 
+        Set to None to hide the context brain. Default is 'midthickness'.
     bmesh_alpha : float, optional
         Opacity of the context brain mesh. Default is 0.2.
     bmesh_color : str, optional
@@ -472,8 +495,8 @@ def plot_tracts(data=None, atlas=None, custom_atlas_path=None, views=None, layou
     bmesh = {}
     if bmesh_type:
         bmesh_path = _resolve_resource_path(bmesh_type, 'bmesh')
-        for h in ['lh', 'rh']:
-            fpath = os.path.join(bmesh_path, f'{bmesh_type}.{h}.gii')
+        for h in ['L', 'R']:
+            fpath = os.path.join(bmesh_path, f'fs_LR.32k.{h}.{bmesh_type}.surf.gii')
             if os.path.exists(fpath):
                 bmesh[h] = load_gii2pv(fpath)
 

{yabplot-0.1.4 → yabplot-0.1.5}/yabplot/scene.py

@@ -91,7 +91,7 @@ def setup_plotter(sel_views, layout, figsize, display_type, needs_bottom_row=Tru
         row_weights = None
 
     plotter = pv.Plotter(shape=(nrows, ncols), groups=groups, row_weights=row_weights,
-                         off_screen=(display_type=='none'), window_size=figsize, border=False)
+                         off_screen=(display_type=='object'), window_size=figsize, border=False)
     plotter.set_background('white')
     return plotter, ncols, nrows
         
@@ -101,7 +101,7 @@ def add_context_to_view(plotter, bmesh, view_side, alpha, color, **kwargs):
     """
     if not bmesh: return
     for h, mesh in bmesh.items():
-        if (view_side == 'L' and h == 'rh') or (view_side == 'R' and h == 'lh'): continue
+        if (view_side == 'L' and h == 'L') or (view_side == 'R' and h == 'R'): continue
         plotter.add_mesh(mesh, color=color, opacity=alpha, 
                          smooth_shading=True, show_edges=False, 
                          **kwargs)
@@ -115,10 +115,19 @@ def set_camera(plotter, view_cfg, zoom=1.0, distance=200):
     plotter.camera.zoom(zoom)
 
 def finalize_plot(plotter, export_path, display_type):
-    if export_path: plotter.screenshot(export_path, transparent_background=True)
+    if export_path: 
+        plotter.screenshot(export_path, transparent_background=True)
     
-    if display_type == 'static': plotter.show(jupyter_backend='static')
-    elif display_type == 'interactive': plotter.show(jupyter_backend='trame')
-    elif display_type == 'none': plotter.close()
-    return plotter
-
+    if display_type == 'static': 
+        out = plotter.show(jupyter_backend='static')
+        plotter.close()
+    elif display_type == 'interactive': 
+        out = plotter.show(jupyter_backend='trame')
+    elif display_type == 'object': 
+        plotter.render()
+        return plotter
+    else:
+        plotter.close()
+        out = None
+    
+    return out

{yabplot-0.1.4 → yabplot-0.1.5}/yabplot/utils.py

@@ -3,6 +3,7 @@ import numpy as np
 import pandas as pd
 import nibabel as nib
 import pyvista as pv
+import scipy.sparse as sp
 import matplotlib.pyplot as plt
 from importlib.resources import files
 
@@ -143,6 +144,93 @@ def map_values_to_surface(data, target_labels, lut_ids, dense_lut_names):
     lookup_table[valid_ids] = source_values
     return lookup_table[target_labels]
 
+def get_adj(faces, n_v):
+    """build adjacency matrix from faces."""
+    row, col = [], []
+    for tri in faces:
+        row.extend([tri[0], tri[1], tri[2], tri[0], tri[1], tri[2]])
+        col.extend([tri[1], tri[2], tri[0], tri[2], tri[0], tri[1]])
+    adj = sp.csc_matrix((np.ones_like(row), (row, col)), shape=(n_v, n_v))
+    adj.data = np.ones_like(adj.data)
+    return adj
+
+def get_smooth_mask(faces, data, iterations=4):
+    """blur binary mask for guide of geometric slicing."""
+    n_v = len(data)
+    mask = data.astype(np.float64)
+    adj = get_adj(faces, n_v)
+    deg = np.array(adj.sum(axis=1)).flatten()
+    deg[deg == 0] = 1.0 
+    for _ in range(iterations):
+        mask = (mask + (adj.dot(mask) / deg)) / 2.0
+    return mask
+
+def apply_internal_blur(faces, data, iterations=1, weight=0.2):
+    """blur data only on borders where different regions touch."""
+    data_out = np.copy(data)
+    n_v = len(data)
+    adj = get_adj(faces, n_v)
+    rows, cols = adj.nonzero()
+    valid = ~np.isnan(data_out)
+    diff = valid[rows] & valid[cols] & ~np.isclose(data_out[rows], data_out[cols], atol=1e-5)
+    b_verts = np.unique(rows[diff])
+    
+    if len(b_verts) == 0: return data_out
+
+    for _ in range(iterations):
+        temp = np.nan_to_num(data_out, nan=0.0)
+        v_counts = adj.dot(valid.astype(float))
+        v_counts[v_counts == 0] = 1.0
+        n_mean = adj.dot(temp) / v_counts
+        data_out[b_verts] = (1 - weight) * data_out[b_verts] + weight * n_mean[b_verts]
+    return data_out
+
+def apply_dilation(faces, data, iterations=4):
+    """push values into NaN space to keep geometric cut pure."""
+    data_out = np.copy(data)
+    n_v = len(data)
+    adj = get_adj(faces, n_v)
+    for _ in range(iterations):
+        nan_m = np.isnan(data_out)
+        temp = np.nan_to_num(data_out, nan=0.0)
+        v_counts = adj.dot((~nan_m).astype(float))
+        s_neighbors = adj.dot(temp)
+        u_mask = nan_m & (v_counts > 0)
+        data_out[u_mask] = s_neighbors[u_mask] / v_counts[u_mask]
+    return data_out
+
+def get_puzzle_pieces(v, f, raw_vals):
+    """carve out geometric pieces with slight overlap to prevent gaps."""
+    pieces = []
+    valid_mask = ~np.isnan(raw_vals) & (raw_vals != 0.0)
+    u_vals = np.unique(raw_vals[valid_mask])
+    master = make_cortical_mesh(v, f, np.zeros_like(raw_vals))
+
+    for val in u_vals:
+        r_mask = np.where(raw_vals == val, 1.0, 0.0)
+        s_mask = get_smooth_mask(f, r_mask, iterations=4)
+        temp = master.copy()
+        temp['Slice_Mask'] = s_mask
+        # reduce search space
+        patch = temp.threshold(0.01, scalars='Slice_Mask')
+        if patch.n_points > 0:
+            # use 0.48 (slightly expanded) for pieces to seal cracks
+            piece = patch.clip_scalar(scalars='Slice_Mask', value=0.48, invert=False)
+            if piece.n_points > 0:
+                piece['Data'] = np.full(piece.n_points, val)
+                pieces.append(piece)
+    
+    # slice base brain
+    all_mask = np.where(valid_mask, 1.0, 0.0)
+    s_all = get_smooth_mask(f, all_mask, iterations=4)
+    master['Slice_Mask'] = s_all
+    # use 0.52 (slightly contracted) for the hole to ensure colored pieces cover the edge
+    base_p = master.clip_scalar(scalars='Slice_Mask', value=0.52, invert=True)
+    if base_p.n_points > 0:
+        base_p['Data'] = np.full(base_p.n_points, np.nan)
+    
+    return base_p, pieces
+
 def lines_from_streamlines(streamlines):
     if len(streamlines) == 0: return np.array([]), np.array([]), np.array([])
     
@@ -155,7 +243,7 @@ def lines_from_streamlines(streamlines):
         cells.append(np.hstack([[length], np.arange(offset, offset + length)]))
     lines = np.hstack(cells)
     
-    # Calculate tangents
+    # calculate tangents
     tangents = []
     for s in streamlines:
         if len(s) < 2: 

{yabplot-0.1.4 → yabplot-0.1.5/yabplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yabplot
-Version: 0.1.4
+Version: 0.1.5
 Summary: yet another brain plot
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -63,32 +63,41 @@ please refer to the [documentation](https://teanijarv.github.io/yabplot/) for mo
 import yabplot as yab
 import numpy as np
 
-# see available cortical atlases
-atlases = yab.get_available_resources(category='cortical')
-
-# see the region names within the aseg atlas
-regions = yab.get_atlas_regions(atlas='aseg', category='subcortical')
-
-# plot data on cortical regions
-data = np.arange(0, 1, 0.001)
-yab.plot_cortical(data=data, atlas='schaefer_1000', figsize=(600, 300),
-                  cmap='viridis', vminmax=[0, 1], style='default',
-                  views=['left_lateral', 'superior', 'right_lateral'])
-
-
-# plot values for specific subcortical regions
-data = {'Left_Amygdala': 0.8, 'Right_Hippocampus': 0.5, 
-        'Right_Thalamus': -0.5, 'Left_Putamen': -1}
-yab.plot_subcortical(data=data, atlas='aseg', figsize=(600, 450), layout=(2, 2),
-                     views=['superior', 'anterior', 'left_lateral', 'right_lateral'], 
-                     cmap='coolwarm', vminmax=[-1, 1], style='matte')
-
-# plot data on white matter bundles
-regions = yab.get_atlas_regions(atlas='xtract_tiny', category='tracts')
-data = np.arange(0, len(regions))
-yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300), 
-                views=['superior', 'anterior', 'left_lateral'], nan_color='#cccccc', 
-                bmesh_type='fsaverage', style='default', cmap='plasma')
+# check that you have the latest version
+print(yab.__version__)
+
+# see available atlases and brain meshes
+print(yab.get_available_resources())
+
+# see the region names for a specific atlas
+print(yab.get_atlas_regions(atlas='aseg', category='subcortical'))
+
+# cortical surfaces
+atlas = 'aparc'
+dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086, ...}
+dmap2 = {'L_fusiform': 0.218, 'L_supramarginal': 0.119, ...}
+yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='midthickness', views=['left_lateral', 'left_medial'],
+                  figsize=(600, 300), cmap='viridis', proc_vertices='sharp')
+yab.plot_cortical(data=dmap2, atlas=atlas, vminmax=[-0.1, 0.3], 
+                  bmesh_type='swm', views=['left_lateral', 'left_medial'],
+                  figsize=(1200, 600), cmap='viridis', proc_vertices='sharp')
+
+# subcortical structures
+atlas = 'aseg'
+regs = yab.get_atlas_regions(atlas=atlas, category='subcortical')
+data = np.arange(1, len(regs)+1)
+yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
+                     views=['left_lateral', 'superior', 'right_lateral'], 
+                     bmesh_alpha=0.1, figsize=(600, 300), cmap='viridis')
+
+# white matter bundles
+atlas = 'xtract_tiny'
+regs = yab.get_atlas_regions(atlas=atlas, category='tracts')
+data = {reg: np.sin(i) for i, reg in enumerate(regs)}
+yab.plot_tracts(data=data, atlas=atlas, style='matte',
+                views=['left_lateral', 'anterior', 'superior'], bmesh_type='pial',
+                bmesh_alpha=0.1, figsize=(1600, 800), cmap='viridis')
 
 ```