Update tutorials to siibra-python v1.0a22

FZJ-INM1-BDA · Dec 17, 2024 · 89d568d · 89d568d
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diff --git a/01-BasicConcepts.ipynb b/01-BasicConcepts.ipynb
@@ -15,7 +15,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a14')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "import os\n",
     "import matplotlib\n",
     "%matplotlib inline"

diff --git a/02-DataFeatures.ipynb b/02-DataFeatures.ipynb
@@ -23,7 +23,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a14')"
+    "assert Version(siibra.__version__) >= Version('1.0a22')"
    ]
   },
   {

diff --git a/03-ProbabilisticAssignment.ipynb b/03-ProbabilisticAssignment.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a14')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "\n",
     "from nilearn import plotting\n",
     "import matplotlib.pyplot as plt\n",
@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "# These are copy-pasted from the interactive atlas viewer:\n",
-    "points = siibra.PointSet(\n",
+    "points = siibra.(\n",
     "    (\n",
     "        [-25.65, -2.75, -33.75],\n",
     "        [-37.35, -81.05, -6.3],\n",

diff --git a/04-DifferentialGeneExpressions.ipynb b/04-DifferentialGeneExpressions.ipynb
@@ -30,7 +30,7 @@
    "source": [
     "import siibra, siibra_jugex\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a14')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "assert Version(siibra_jugex.__version__) >= Version(\"1.2\")"
    ]
   },

diff --git a/05-CombinedWorkflow.ipynb b/05-CombinedWorkflow.ipynb
@@ -20,7 +20,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a14')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib notebook"

diff --git a/06-CorticalPatchSampling.ipynb b/06-CorticalPatchSampling.ipynb
@@ -9,7 +9,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a17')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib notebook\n",
     "import numpy as np\n",
@@ -202,7 +202,7 @@
     "l4layer = layers.get_region(f\"4 {hemisphere}\")\n",
     "\n",
     "# collect all layer IV contour points into one set\n",
-    "l4points = siibra.PointSet(\n",
+    "l4points = siibra.(\n",
     "    [p for contour in layer_contours[l4layer.name] for p in contour], \n",
     "    space='bigbrain'\n",
     ")\n",

diff --git a/workshops/BigBrainWorkshop2023.ipynb b/workshops/BigBrainWorkshop2023.ipynb
@@ -17,7 +17,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a17')"
+    "assert Version(siibra.__version__) >= Version('1.0a22')"
    ]
   },
   {
@@ -159,7 +159,7 @@
    "outputs": [],
    "source": [
     "# we can directly instantiate a location object from the structure in siibra\n",
-    "# the annotation is cast to a siibra pointset.\n",
+    "# the annotation is cast to a siibra .\n",
     "# Note that it has already the proper reference space encoded!\n",
     "points = siibra.from_json(structure)\n",
     "print(points)"

diff --git a/workshops/HIBALL-winterschool-2023.ipynb b/workshops/HIBALL-winterschool-2023.ipynb
@@ -17,7 +17,7 @@
    "source": [
     "import siibra\n",
     "from packaging.version import Version\n",
-    "assert Version(siibra.__version__) >= Version('1.0a17')\n",
+    "assert Version(siibra.__version__) >= Version('1.0a22')\n",
     "\n",
     "import matplotlib\n",
     "from nilearn import plotting\n",
@@ -801,7 +801,7 @@
    "outputs": [],
    "source": [
     "# We can plot the MNI coordinates to localize the measures and verify they are located in V1.\n",
-    "locations = siibra.PointSet(features[0].data.mni_xyz.tolist(), space=\"mni152\")\n",
+    "locations = siibra.(features[0].data.mni_xyz.tolist(), space=\"mni152\")\n",
     "\n",
     "from nilearn import plotting\n",
     "mask = v1.get_regional_map(\"mni152\")\n",

diff --git a/workshops/imb9345-2024.ipynb b/workshops/imb9345-2024.ipynb
@@ -33,7 +33,7 @@
    "source": [
     "import siibra as sb\n",
     "from packaging.version import Version\n",
-    "assert Version(sb.__version__) >= Version('1.0a18')\n",
+    "assert Version(sb.__version__) >= Version('1.0a22')\n",
     "from nilearn import plotting\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib notebook"

diff --git a/workshops/ohbm-2023-example.ipynb b/workshops/ohbm-2023-example.ipynb
@@ -23,7 +23,7 @@
    "source": [
     "import siibra as sb\n",
     "from packaging.version import Version\n",
-    "assert Version(sb.__version__) >= Version('1.0a18')\n",
+    "assert Version(sb.__version__) >= Version('1.0a22')\n",
     "from nilearn import plotting\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib notebook"