going to v0.2a6, with WHS4

dickscheid · dickscheid · commit 83783446916c · 2021-10-08T23:36:12.000+02:00
diff --git a/docs/download_maps.ipynb b/docs/download_maps.ipynb
@@ -18,7 +18,7 @@
    "outputs": [],
    "source": [
     "import siibra\n",
-    "atlas = siibra.atlasesMULTILEVEL_HUMAN_ATLAS"
+    "atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS"
    ]
   },
   {
@@ -89,13 +89,6 @@
     "        if mapindex>4:\n",
     "            break"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -119,4 +112,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/Different species.ipynb b/examples/Different species.ipynb
@@ -3,7 +3,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7356f741",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +13,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dd04581c",
    "metadata": {},
    "source": [
     "# Allen mouse brain atlas"
@@ -23,7 +21,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e161329",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -35,7 +32,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4dcc9ab2",
    "metadata": {},
    "source": [
     "# Waxholm space atlas of the sprague dawley rat brain"
@@ -44,27 +40,25 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14b37103",
    "metadata": {},
    "outputs": [],
    "source": [
     "atlas = siibra.atlases['waxholm rat']\n",
     "waxholmtpl = atlas.get_template().fetch()\n",
-    "parcellationmap = atlas.get_map().fetch()\n",
-    "plotting.plot_roi(parcellationmap,bg_img=waxholmtpl,cmap=\"Set1\")"
+    "for v in [\"v3\",\"v4\"]:\n",
+    "    parcellationmap = atlas.get_map(parcellation=v).fetch()\n",
+    "    plotting.plot_roi(parcellationmap,bg_img=waxholmtpl,cmap=\"Set2\")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "0ba085f9",
    "metadata": {},
    "source": [
     "# Human brain atlas"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "302bbad1",
    "metadata": {},
    "source": [
     "## MNI space"
@@ -73,11 +67,10 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "94542ae6",
    "metadata": {},
    "outputs": [],
    "source": [
-    "atlas = siibra.atlasesMULTILEVEL_HUMAN_ATLAS\n",
+    "atlas = siibra.atlases['human']\n",
     "mni152tpl = atlas.get_template(\"mni152\").fetch()\n",
     "parcellationmap = atlas.get_map(space=\"mni152\", parcellation=\"julich 2.9\")\n",
     "for img in parcellationmap.fetch_iter():\n",
@@ -86,7 +79,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "02c1e45a",
    "metadata": {},
    "source": [
     "## BigBrain space"
@@ -95,7 +87,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "522ce332",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +99,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b090eab3",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/examples/Find areas and their connections.ipynb b/examples/Find areas and their connections.ipynb
@@ -56,7 +56,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "atlas = siibra.atlasesMULTILEVEL_HUMAN_ATLAS\n",
+    "atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS\n",
     "julich_pmaps = atlas.get_map(\n",
     "    space=\"mni152\",\n",
     "    parcellation=\"julich 2.9\",\n",
diff --git a/examples/Retrieve multimodal data features.ipynb b/examples/Retrieve multimodal data features.ipynb
@@ -2,7 +2,6 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "c1232d7c",
    "metadata": {
     "slideshow": {
      "slide_type": "slide"
@@ -17,7 +16,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ff9e6a34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +25,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7fd9ae52",
    "metadata": {},
    "source": [
     "### 1. Setup `siibra` to connect to the EBRAINS Knowledge Graph access token\n",
@@ -47,7 +44,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e2a81972",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -57,7 +53,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "58815182",
    "metadata": {},
    "source": [
     "### 2. Extract transmitter receptor densities\n",
@@ -70,11 +65,10 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c10eeaf7",
    "metadata": {},
    "outputs": [],
    "source": [
-    "atlas = siibra.atlasesMULTILEVEL_HUMAN_ATLAS\n",
+    "atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS\n",
     "features = siibra.get_features(\n",
     "    atlas.get_parcellation('julich'),\n",
     "    siibra.modalities.ReceptorDistribution)\n",
@@ -84,7 +78,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "df6aab97",
    "metadata": {},
    "source": [
     "If we select a region, the returned list is filtered accordingly. "
@@ -93,7 +86,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ec00e841",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -103,7 +95,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e91d9e5e",
    "metadata": {},
    "source": [
     "### 3. Cell distributions\n",
@@ -114,7 +105,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0b5eab2f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +122,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "824ea6db",
    "metadata": {
     "slideshow": {
      "slide_type": "slide"
@@ -147,7 +136,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "669cc089",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +160,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "593d7be2",
    "metadata": {
     "slideshow": {
      "slide_type": "slide"
@@ -188,7 +175,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6733fab6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,7 +201,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "32082ebb",
    "metadata": {},
    "source": [
     "### 6. Retrieving iEEG electrodes and contact points\n",
@@ -226,7 +211,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "88c2ae6e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -253,7 +237,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f365cfd8",
    "metadata": {},
    "source": [
     "### 7. Retrieving other types of regional datasets from EBRAINS"
@@ -262,14 +245,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ba2cbdb3",
    "metadata": {},
    "outputs": [],
    "source": [
     "region = atlas.get_region(\"fp1 right\")\n",
     "for f in siibra.get_features(region, \"ebrains\"):\n",
     "    print(f\"{f.name}\\n{f.url}\\n\")"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/examples/Walkthrough.ipynb b/examples/Walkthrough.ipynb
@@ -372,13 +372,6 @@
     "for f in features:\n",
     "    print(f.name)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/siibra/volumes/volume.py b/siibra/volumes/volume.py
@@ -21,7 +21,7 @@
 
 from ctypes import ArgumentError
 import numpy as np
-from nibabel import Nifti1Image
+import nibabel
 from cloudvolume.exceptions import OutOfBoundsError
 from cloudvolume import CloudVolume
 import os
@@ -170,7 +170,7 @@ class LocalNiftiVolume(ImageProvider):
 
     volume_type = 'nii'
 
-    def __init__(self, name: str, img: Nifti1Image, space: Space):
+    def __init__(self, name: str, img: nibabel.Nifti1Image, space: Space):
         """ Create a new local nifti volume from a Nifti1Image object.
 
         Args:
@@ -179,12 +179,19 @@ def __init__(self, name: str, img: Nifti1Image, space: Space):
             space (Space): the reference space associated with the Image
         """
         self.name = name
-        if isinstance(img, Nifti1Image):
+        if isinstance(img, nibabel.Nifti1Image):
             self.image = img
         elif isinstance(img, str): 
-            self.image = Nifti1Image.from_filename(img)
+            self.image = nibabel.load(img)
         else:
             raise ValueError(f"Cannot create local nifti volume from image parameter {img}") 
+
+        if np.isnan(self.image.get_fdata()).any():
+            logger.warn(f'Replacing NaN by 0 for {self.name}')
+            self.image = nibabel.Nifti1Image(
+                np.nan_to_num(self.image.get_fdata()),
+                self.image.affine
+            )
         self.space = space
 
     def fetch(self, **kwargs):
@@ -249,7 +256,7 @@ def fetch(self, resolution_mm=None, voi=None, mapindex=None, clip=False):
                 f"Mapindex of {mapindex} provided for fetching from NiftiVolume, but its shape is {shape}."
             )
         else:
-            img = Nifti1Image(
+            img = nibabel.Nifti1Image(
                 dataobj=self.image.dataobj[:, :, :, mapindex], affine=self.image.affine
             )
         assert img is not None
@@ -265,7 +272,7 @@ def fetch(self, resolution_mm=None, voi=None, mapindex=None, clip=False):
             (x0, y0, z0), (x1, y1, z1) = bb_vox.minpoint, bb_vox.maxpoint
             shift = np.identity(4)
             shift[:3, -1] = bb_vox.minpoint
-            img = Nifti1Image(
+            img = nibabel.Nifti1Image(
                 dataobj=img.dataobj[x0:x1, y0:y1, z0:z1],
                 affine=np.dot(img.affine, shift),
             )
@@ -526,7 +533,7 @@ def fetch(self, resolution_mm=None, voi=None, mapindex=None, clip=False):
         if data.ndim == 2:
             data = data.reshape(list(data.shape) + [1])
 
-        return Nifti1Image(data, self.build_affine(resolution_mm=resolution_mm, voi=voi))
+        return nibabel.Nifti1Image(data, self.build_affine(resolution_mm=resolution_mm, voi=voi))
 
     def get_shape(self, resolution_mm=None):
         mip = self._resolution_to_mip(resolution_mm, voi=None)
diff --git a/test/features/test_connectivity.py b/test/features/test_connectivity.py
@@ -32,7 +32,7 @@ def test_check_switch_parc(self):
 class TestConnectivity(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        atlas = siibra.atlases["human"]
+        atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS
         parcellation = atlas.get_parcellation(
             siibra.parcellations.JULICH_BRAIN_CYTOARCHITECTONIC_MAPS_1_18
         )
diff --git a/test/features/test_ebrainsquery.py b/test/features/test_ebrainsquery.py
diff --git a/test/features/test_extract_transmitter_receptor_densities.py b/test/features/test_extract_transmitter_receptor_densities.py

Original file line number	Diff line number	Diff line change
`@@ -372,13 +372,6 @@`
`372`	`372`	`"for f in features:\n",`
`373`	`373`	`" print(f.name)"`
`374`	`374`	`]`
`375`		`- },`
`376`		`- {`
`377`		`- "cell_type": "code",`
`378`		`- "execution_count": null,`
`379`		`- "metadata": {},`
`380`		`- "outputs": [],`
`381`		`- "source": []`
`382`	`375`	`}`
`383`	`376`	`],`
`384`	`377`	`"metadata": {`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@ def test_check_switch_parc(self):`
`32`	`32`	`class TestConnectivity(unittest.TestCase):`
`33`	`33`	`@classmethod`
`34`	`34`	`def setUpClass(cls):`
`35`		`- atlas = siibra.atlases["human"]`
	`35`	`+ atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS`
`36`	`36`	`parcellation = atlas.get_parcellation(`
`37`	`37`	`siibra.parcellations.JULICH_BRAIN_CYTOARCHITECTONIC_MAPS_1_18`
`38`	`38`	`)`