more brain meshes, cortical plotting finetuning

Author: teanijarv

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')
 
 ```
 

docs/assets/examples.png

@@ -139,7 +139,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": null,
    "id": "63863fc7",
    "metadata": {},
    "outputs": [
@@ -198,7 +198,7 @@
     "\n",
     "# run the parser\n",
     "lut_path = os.path.join(work_dir, \"brainnetome.txt\")\n",
-    "parse_brainnetome_xml(aal_xml, lut_path)"
+    "parse_brainnetome_xml(a_xml, lut_path)"
    ]
   },
   {
@@ -217,7 +217,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": null,
    "id": "d7aa2945",
    "metadata": {},
    "outputs": [
@@ -336,11 +336,11 @@
     "print(\"--- step 3: processing hemispheres ---\")\n",
     "\n",
     "# 1. map & refine left hemisphere\n",
-    "lh_raw = map_volume_to_surface(aal_nii, surf_data['lh']['surf'])\n",
+    "lh_raw = map_volume_to_surface(a_nii, surf_data['lh']['surf'])\n",
     "lh_final = refine_surface_map(lh_raw, surf_data['lh']['surf'], surf_data['lh']['mask'])\n",
     "\n",
     "# 2. map & refine right hemisphere\n",
-    "rh_raw = map_volume_to_surface(aal_nii, surf_data['rh']['surf'])\n",
+    "rh_raw = map_volume_to_surface(a_nii, surf_data['rh']['surf'])\n",
     "rh_final = refine_surface_map(rh_raw, surf_data['rh']['surf'], surf_data['rh']['mask'])\n",
     "\n",
     "# 3. save final csv\n",

docs/tutorials/available_atlases.ipynb

@@ -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"

docs/tutorials/custom_cortical_atlas.ipynb

@@ -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)

docs/tutorials/getting_started.ipynb

@@ -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