Merge pull request #211 from jhlegarreta/AddPyBIDSLeadingDotWarning

ENH: Add PyBIDS leading dot warning

_episodes/constrained_spherical_deconvolution.md

@@ -58,31 +58,27 @@ import os
 import nibabel as nib
 import numpy as np
 
-import bids
 from bids.layout import BIDSLayout
 
 from dipy.core.gradients import gradient_table
 from dipy.data import default_sphere
 from dipy.io.gradients import read_bvals_bvecs
 from dipy.io.image import load_nifti
 
-
-bids.config.set_option('extension_initial_dot', True)
-
 dwi_layout = BIDSLayout('../../data/ds000221/derivatives/uncorrected_topup_eddy/', validate=False)
 t1_layout = BIDSLayout('../../data/ds000221/derivatives/uncorrected_topup_eddy_regT1/', validate=False)
 gradient_layout = BIDSLayout('../../data/ds000221/sub-010006/ses-01/dwi/', validate=False)
 
 subj = '010006'
 
 # Get the diffusion files
-dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]
-bvec_fname = dwi_layout.get(subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]
-bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='bval', return_type='file')[0]
+dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]
+bvec_fname = dwi_layout.get(subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]
+bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]
 
 
 # Get the anatomical file
-t1w_fname = t1_layout.get(subject=subj, extension='nii.gz', return_type='file')[0]
+t1w_fname = t1_layout.get(subject=subj, extension='.nii.gz', return_type='file')[0]
 
 data, affine = load_nifti(dwi_fname)
 

_episodes/deterministic_tractography.md

@@ -28,23 +28,19 @@ import os
 import nibabel as nib
 import numpy as np
 
-import bids
 from bids.layout import BIDSLayout
 
 from dipy.io.gradients import read_bvals_bvecs
 from dipy.core.gradients import gradient_table
 
-
-bids.config.set_option('extension_initial_dot', True)
-
 dwi_layout = BIDSLayout("../../data/ds000221/derivatives/uncorrected_topup_eddy", validate=False)
 gradient_layout = BIDSLayout("../../data/ds000221/", validate=False)
 
 subj = '010006'
 
-dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]
-bvec_fname = dwi_layout.get(subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]
-bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='bval', return_type='file')[0]
+dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]
+bvec_fname = dwi_layout.get(subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]
+bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]
 
 dwi_img = nib.load(dwi_fname)
 affine = dwi_img.affine
@@ -274,9 +270,9 @@ plt.show()
 > > 
 > > # Get subject data
 > > subj = '010006'
-> > dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]
-> > bvec_fname = dwi_layout.get(subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]
-> > bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='bval', return_type='file')[0]
+> > dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]
+> > bvec_fname = dwi_layout.get(subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]
+> > bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]
 > > 
 > > dwi_img = nib.load(dwi_fname)
 > > affine = dwi_img.affine

_episodes/diffusion_tensor_imaging.md

@@ -104,19 +104,16 @@ and load them! We will also load in the anatomical image to use as a reference
 later on.
 
 ~~~
-import bids
 from bids.layout import BIDSLayout
 from dipy.io.gradients import read_bvals_bvecs
 from dipy.core.gradients import gradient_table
 from nilearn import image as img
 
-bids.config.set_option('extension_initial_dot', True)
-
 deriv_layout = BIDSLayout("../data/ds000221/derivatives", validate=False)
 subj="010006"
 
 # Grab the transformed t1 file for reference
-t1 = deriv_layout.get(subject=subj, space="dwi", extension='nii.gz', return_type='file')[0]
+t1 = deriv_layout.get(subject=subj, space="dwi", extension='.nii.gz', return_type='file')[0]
 
 # Recall the preprocessed data is no longer in BIDS - we will directly grab these files
 dwi = f"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.nii.gz"
@@ -322,7 +319,7 @@ data!
 > > deriv_layout = BIDSLayout("../data/ds000221/derivatives", validate=False)
 > > subj="010006"
 > >
-> > t1 = deriv_layout.get(subject=subj, space="dwi", extension='nii.gz', return_type='file')[0]
+> > t1 = deriv_layout.get(subject=subj, space="dwi", extension='.nii.gz', return_type='file')[0]
 > > dwi = f"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.nii.gz"
 > > bval = f"../data/ds000221/sub-{subj}/ses-01/dwi/sub-{subj}_ses-01_dwi.bval"
 > > bvec = f"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.eddy_rotated_bvecs"

_episodes/introduction.md

@@ -133,13 +133,10 @@ Let's first pull the metadata from its associated JSON file using the
 <code>get_metadata()</code> function for the first run.
 
 ~~~
-import bids
 from bids.layout import BIDSLayout
 
 ?BIDSLayout
 
-bids.config.set_option('extension_initial_dot', True)
-
 layout = BIDSLayout("../data/ds000221", validate=False)
 ~~~
 {: .language-python}
@@ -148,7 +145,7 @@ Now that we have a layout object, we can work with a BIDS dataset! Let's
 extract the metadata from the dataset.
 
 ~~~
-dwi = layout.get(subject='010006', suffix='dwi', extension='nii.gz', return_type='file')[0]
+dwi = layout.get(subject='010006', suffix='dwi', extension='.nii.gz', return_type='file')[0]
 layout.get_metadata(dwi)
 ~~~
 {: .language-python}
@@ -377,7 +374,7 @@ axonal trajectories via tractography.
 > > ## Solution
 > >
 > > ~~~
-> > dwi_data = layout.get(suffix='dwi', extension='nii.gz', return_type='file')
+> > dwi_data = layout.get(suffix='dwi', extension='.nii.gz', return_type='file')
 > > ~~~
 > > {: .language-python}
 > {: .solution}

_episodes/preprocessing.md

@@ -53,20 +53,17 @@ image to use later on, as well as the second inversion from the anatomical
 acquisition for brainmasking purposes.
 
 ~~~
-import bids
 from bids.layout import BIDSLayout
 
-bids.config.set_option('extension_initial_dot', True)
-
 layout = BIDSLayout("../../data/ds000221", validate=False)
 
 subj='010006'
 
 # Diffusion data
-dwi = layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]
+dwi = layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]
 
 # Anatomical data
-t1w = layout.get(subject=subj, suffix='T1w', extension='nii.gz', return_type='file')[0]
+t1w = layout.get(subject=subj, suffix='T1w', extension='.nii.gz', return_type='file')[0]
 ~~~
 {: .language-python}
 

_episodes/probabilistic_tractography.md

@@ -51,24 +51,19 @@ import os
 import nibabel as nib
 import numpy as np
 
-import bids
 from bids.layout import BIDSLayout
 
 from dipy.core.gradients import gradient_table
-from dipy.data import get_fnames
 from dipy.io.gradients import read_bvals_bvecs
 
-
-bids.config.set_option('extension_initial_dot', True)
-
 dwi_layout = BIDSLayout('../../data/ds000221/derivatives/uncorrected_topup_eddy/', validate=False)
 gradient_layout = BIDSLayout('../../data/ds000221/', validate=False)
 
 subj = '010006'
 
-dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]
-bvec_fname = dwi_layout.get(subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]
-bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='bval', return_type='file')[0]
+dwi_fname = dwi_layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]
+bvec_fname = dwi_layout.get(subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]
+bval_fname = gradient_layout.get(subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]
 
 dwi_img = nib.load(dwi)
 affine = dwi_img.affine

code/constrained_spherical_deconvolution.ipynb

@@ -39,17 +39,13 @@
     "import nibabel as nib\n",
     "import numpy as np\n",
     "\n",
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "\n",
     "from dipy.core.gradients import gradient_table\n",
     "from dipy.data import default_sphere\n",
     "from dipy.io.gradients import read_bvals_bvecs\n",
     "from dipy.io.image import load_nifti\n",
     "\n",
-    "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "dwi_layout = BIDSLayout(\n",
     "    '../data/ds000221/derivatives/uncorrected_topup_eddy/', validate=False)\n",
     "t1_layout = BIDSLayout(\n",
@@ -61,16 +57,16 @@
     "\n",
     "# Get the diffusion files\n",
     "dwi_fname = dwi_layout.get(subject=subj, suffix='dwi',\n",
-    "                           extension='nii.gz', return_type='file')[0]\n",
+    "                           extension='.nii.gz', return_type='file')[0]\n",
     "bvec_fname = dwi_layout.get(\n",
-    "    subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]\n",
+    "    subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]\n",
     "bval_fname = gradient_layout.get(\n",
-    "    subject=subj, suffix='dwi', extension='bval', return_type='file')[0]\n",
+    "    subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]\n",
     "\n",
     "\n",
     "# Get the anatomical file\n",
     "t1w_fname = t1_layout.get(\n",
-    "    subject=subj, extension='nii.gz', return_type='file')[0]\n",
+    "    subject=subj, extension='.nii.gz', return_type='file')[0]\n",
     "\n",
     "data, affine = load_nifti(dwi_fname)\n",
     "\n",

code/deterministic_tractography.ipynb

@@ -22,27 +22,23 @@
     "import nibabel as nib\n",
     "import numpy as np\n",
     "\n",
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "\n",
     "from dipy.io.gradients import read_bvals_bvecs\n",
     "from dipy.core.gradients import gradient_table\n",
     "\n",
-    "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "dwi_layout = BIDSLayout(\n",
     "    \"../data/ds000221/derivatives/uncorrected_topup_eddy\", validate=False)\n",
     "gradient_layout = BIDSLayout(\"../data/ds000221/\", validate=False)\n",
     "\n",
     "subj = '010006'\n",
     "\n",
     "dwi_fname = dwi_layout.get(subject=subj, suffix='dwi',\n",
-    "                           extension='nii.gz', return_type='file')[0]\n",
+    "                           extension='.nii.gz', return_type='file')[0]\n",
     "bvec_fname = dwi_layout.get(\n",
-    "    subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]\n",
+    "    subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]\n",
     "bval_fname = gradient_layout.get(\n",
-    "    subject=subj, suffix='dwi', extension='bval', return_type='file')[0]\n",
+    "    subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]\n",
     "\n",
     "dwi_img = nib.load(dwi_fname)\n",
     "affine = dwi_img.affine\n",
@@ -333,11 +329,11 @@
     "# Get subject data\n",
     "subj = '010006'\n",
     "dwi_fname = dwi_layout.get(subject=subj, suffix='dwi',\n",
-    "                           extension='nii.gz', return_type='file')[0]\n",
+    "                           extension='.nii.gz', return_type='file')[0]\n",
     "bvec_fname = dwi_layout.get(\n",
-    "    subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]\n",
+    "    subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]\n",
     "bval_fname = gradient_layout.get(\n",
-    "    subject=subj, suffix='dwi', extension='bval', return_type='file')[0]\n",
+    "    subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]\n",
     "\n",
     "dwi_img = nib.load(dwi_fname)\n",
     "affine = dwi_img.affine\n",

code/diffusion_tensor_imaging.ipynb

@@ -61,20 +61,17 @@
    "cell_type": "code",
    "execution_count": null,
    "source": [
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "from dipy.io.gradients import read_bvals_bvecs\n",
     "from dipy.core.gradients import gradient_table\n",
     "from nilearn import image as img\n",
     "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "deriv_layout = BIDSLayout(\"../data/ds000221/derivatives\", validate=False)\n",
     "subj = \"010006\"\n",
     "\n",
     "# Grab the transformed t1 file for reference\n",
     "t1 = deriv_layout.get(subject=subj, space=\"dwi\",\n",
-    "                      extension='nii.gz', return_type='file')[0]\n",
+    "                      extension='.nii.gz', return_type='file')[0]\n",
     "\n",
     "# Recall the preprocessed data is no longer in BIDS - we will directly grab these files\n",
     "dwi = f\"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.nii.gz\"\n",
@@ -291,7 +288,7 @@
     "subj = \"010006\"\n",
     "\n",
     "t1 = deriv_layout.get(subject=subj, space=\"dwi\",\n",
-    "                      extension='nii.gz', return_type='file')[0]\n",
+    "                      extension='.nii.gz', return_type='file')[0]\n",
     "dwi = f\"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.nii.gz\"\n",
     "bval = f\"../data/ds000221/sub-{subj}/ses-01/dwi/sub-{subj}_ses-01_dwi.bval\"\n",
     "bvec = f\"../data/ds000221/derivatives/uncorrected_topup_eddy/sub-{subj}/ses-01/dwi/dwi.eddy_rotated_bvecs\"\n",

code/introduction.ipynb

@@ -115,13 +115,10 @@
    "cell_type": "code",
    "execution_count": null,
    "source": [
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "\n",
     "?BIDSLayout\n",
     "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "layout = BIDSLayout(\"../data/ds000221\", validate=False)"
    ],
    "outputs": [],
@@ -140,7 +137,7 @@
    "cell_type": "code",
    "execution_count": null,
    "source": [
-    "dwi = layout.get(subject='010006', suffix='dwi', extension='nii.gz', return_type='file')[0]\n",
+    "dwi = layout.get(subject='010006', suffix='dwi', extension='.nii.gz', return_type='file')[0]\n",
     "layout.get_metadata(dwi)"
    ],
    "outputs": [],
@@ -336,7 +333,7 @@
    "cell_type": "code",
    "execution_count": null,
    "source": [
-    "dwi_data = layout.get(suffix='dwi', extension='nii.gz', return_type='file')"
+    "dwi_data = layout.get(suffix='dwi', extension='.nii.gz', return_type='file')"
    ],
    "outputs": [],
    "metadata": {

code/preprocessing.ipynb

@@ -33,20 +33,17 @@
    "cell_type": "code",
    "execution_count": null,
    "source": [
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "layout = BIDSLayout(\"../data/ds000221\", validate=False)\n",
     "\n",
     "subj='010006'\n",
     "\n",
     "# Diffusion data\n",
-    "dwi = layout.get(subject=subj, suffix='dwi', extension='nii.gz', return_type='file')[0]\n",
+    "dwi = layout.get(subject=subj, suffix='dwi', extension='.nii.gz', return_type='file')[0]\n",
     "\n",
     "# Anatomical data\n",
-    "t1w = layout.get(subject=subj, suffix='T1w', extension='nii.gz', return_type='file')[0]"
+    "t1w = layout.get(subject=subj, suffix='T1w', extension='.nii.gz', return_type='file')[0]"
    ],
    "outputs": [],
    "metadata": {}

code/probabilistic_tractography.ipynb

@@ -45,15 +45,11 @@
     "import nibabel as nib\n",
     "import numpy as np\n",
     "\n",
-    "import bids\n",
     "from bids.layout import BIDSLayout\n",
     "\n",
     "from dipy.core.gradients import gradient_table\n",
     "from dipy.io.gradients import read_bvals_bvecs\n",
     "\n",
-    "\n",
-    "bids.config.set_option('extension_initial_dot', True)\n",
-    "\n",
     "# Get the diffusion files\n",
     "dwi_layout = BIDSLayout(\n",
     "    '../data/ds000221/derivatives/uncorrected_topup_eddy/', validate=False)\n",
@@ -63,11 +59,11 @@
     "subj = '010006'\n",
     "\n",
     "dwi_fname = dwi_layout.get(subject=subj, suffix='dwi',\n",
-    "                           extension='nii.gz', return_type='file')[0]\n",
+    "                           extension='.nii.gz', return_type='file')[0]\n",
     "bval_fname = gradient_layout.get(\n",
-    "    subject=subj, suffix='dwi', extension='bval', return_type='file')[0]\n",
+    "    subject=subj, suffix='dwi', extension='.bval', return_type='file')[0]\n",
     "bvec_fname = dwi_layout.get(\n",
-    "    subject=subj, extension='eddy_rotated_bvecs', return_type='file')[0]\n",
+    "    subject=subj, extension='.eddy_rotated_bvecs', return_type='file')[0]\n",
     "\n",
     "dwi_img = nib.load(dwi_fname)\n",
     "affine = dwi_img.affine\n",

requirements.txt

@@ -3,4 +3,4 @@ fury==0.6.1
 matplotlib
 nilearn==0.7.0
 osfclient==0.0.5
-pybids==0.12.4
+pybids==0.14.0