Commit 03af5f3f authored by Michiel Cottaar's avatar Michiel Cottaar
Browse files

Replace mcutils with mcot

parent fed6ea08
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...@@ -2,7 +2,6 @@ before_script: ...@@ -2,7 +2,6 @@ before_script:
- apt-get update -qq - apt-get update -qq
- apt-get install python3 - apt-get install python3
- pip install numpy pandas seaborn - pip install numpy pandas seaborn
- pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/mcutils.git
- pip install . - pip install .
- pip install pytest - pip install pytest
......
...@@ -11,7 +11,6 @@ Installation ...@@ -11,7 +11,6 @@ Installation
The requirements can be installed using conda and pip: The requirements can be installed using conda and pip:
```sh ```sh
conda install -c conda-forge nibabel scipy sympy conda install -c conda-forge nibabel scipy sympy
pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/mcutils.git
pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure.git pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure.git
``` ```
......
...@@ -7,7 +7,6 @@ Gyral structure can be installed using pip: ...@@ -7,7 +7,6 @@ Gyral structure can be installed using pip:
.. code-block:: sh .. code-block:: sh
pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/mcutils.git
pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure.git pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure.git
You can view the code at https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure You can view the code at https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure
...@@ -80,7 +79,7 @@ After defining the command line interface we start by importing the libraries: ...@@ -80,7 +79,7 @@ After defining the command line interface we start by importing the libraries:
import nibabel as nib import nibabel as nib
import numpy as np import numpy as np
from gyral_structure import basis, cost, request from gyral_structure import basis, cost, request
from mcutils.surface import CorticalMesh, grid from mcot.surface import CorticalMesh, grid
Requests: where to evaluate the cost function Requests: where to evaluate the cost function
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
Produces several QC plots for surfaces Produces several QC plots for surfaces
""" """
from mcutils.surface import CorticalMesh from mcot.surface import CorticalMesh
from gyral_structure.request import read_surface from gyral_structure.request import read_surface
from gyral_structure.basis import BasisFunc from gyral_structure.basis import BasisFunc
from nibabel import cifti2 from nibabel import cifti2
......
...@@ -16,7 +16,7 @@ in multiple cost functions. ...@@ -16,7 +16,7 @@ in multiple cost functions.
import scipy as sp import scipy as sp
import itertools import itertools
from itertools import zip_longest from itertools import zip_longest
from mcutils.surface import CorticalMesh from mcot.surface import CorticalMesh
import nibabel import nibabel
import os import os
from numpy import linalg from numpy import linalg
......
...@@ -20,8 +20,8 @@ args = parser.parse_args() ...@@ -20,8 +20,8 @@ args = parser.parse_args()
import nibabel import nibabel
import numpy as np import numpy as np
from gyral_structure import basis, streamline from gyral_structure import basis, streamline
from mcutils.surface import CorticalMesh, grid from mcot.surface import CorticalMesh, grid
from mcutils.utils.write_gifti import write_gifti from mcot.surface import write_gifti
from numpy import linalg from numpy import linalg
from scipy import ndimage from scipy import ndimage
......
...@@ -10,9 +10,9 @@ args = parser.parse_args() ...@@ -10,9 +10,9 @@ args = parser.parse_args()
import nibabel import nibabel
from gyral_structure import basis, request, utils from gyral_structure import basis, request, utils
from mcutils.surface import CorticalMesh from mcot.surface import CorticalMesh
import scipy as sp import scipy as sp
import cifti from nibabel import cifti2
basis_func, best_fit_arr = basis.read(args.field) basis_func, best_fit_arr = basis.read(args.field)
img = nibabel.load(args.surface) img = nibabel.load(args.surface)
...@@ -34,6 +34,6 @@ for idx in range(arr_triangle.shape[0]): ...@@ -34,6 +34,6 @@ for idx in range(arr_triangle.shape[0]):
conn, val = sp.broadcast_arrays(surf.faces, arr_triangle[idx][None, :]) conn, val = sp.broadcast_arrays(surf.faces, arr_triangle[idx][None, :])
nconn = sp.bincount(conn.flatten(), minlength=surf.nvertices) nconn = sp.bincount(conn.flatten(), minlength=surf.nvertices)
arr_vertices[idx] = sp.bincount(conn.flatten(), val.flatten(), minlength=surf.nvertices) / nconn arr_vertices[idx] = sp.bincount(conn.flatten(), val.flatten(), minlength=surf.nvertices) / nconn
bm = cifti.BrainModel.from_mask(mask, name=img.darrays[0].metadata['AnatomicalStructurePrimary']) bm = cifti2.BrainModelAxis.from_mask(mask, name=img.darrays[0].metadata['AnatomicalStructurePrimary'])
cifti.write(args.output, arr_vertices, (cifti.Scalar.from_names(['density (crossing)', 'density (total)', 'radiality', 'x', 'y', 'z']), bm)) cifti2.Cifti2Image(arr_vertices, (cifti2.ScalarAxis(['density (crossing)', 'density (total)', 'radiality', 'x', 'y', 'z']), bm)).to_filename(args.output)
...@@ -41,7 +41,7 @@ args = parser.parse_args() ...@@ -41,7 +41,7 @@ args = parser.parse_args()
import nibabel as nib import nibabel as nib
import numpy as np import numpy as np
from gyral_structure import basis, cost, request, utils from gyral_structure import basis, cost, request, utils
from mcutils.surface import CorticalMesh, grid, Cortex from mcot.surface import CorticalMesh, grid, Cortex
from warnings import warn from warnings import warn
from nibabel import affines from nibabel import affines
......
...@@ -25,7 +25,7 @@ parser.add_argument("-N", "--norient", default=300, type=int, ...@@ -25,7 +25,7 @@ parser.add_argument("-N", "--norient", default=300, type=int,
"default: 300") "default: 300")
args = parser.parse_args() args = parser.parse_args()
from mcutils.surface import CorticalMesh, grid, orientation from mcot.surface import CorticalMesh, grid, orientation
import nibabel as nib import nibabel as nib
import numpy as np import numpy as np
from scipy import ndimage from scipy import ndimage
......
...@@ -24,7 +24,7 @@ parser.add_argument("-sp", "--skip_plots", action='store_true', ...@@ -24,7 +24,7 @@ parser.add_argument("-sp", "--skip_plots", action='store_true',
args = parser.parse_args() args = parser.parse_args()
from gyral_structure.basis import read from gyral_structure.basis import read
from mcutils.surface import CorticalMesh, Cortex from mcot.surface import CorticalMesh, Cortex
import os import os
from gyral_structure import qc from gyral_structure import qc
import nibabel as nib import nibabel as nib
......
...@@ -17,7 +17,7 @@ if len(args.stop) % 2 != 0: ...@@ -17,7 +17,7 @@ if len(args.stop) % 2 != 0:
import nibabel import nibabel
from numpy import linalg from numpy import linalg
from gyral_structure import basis, request, streamline from gyral_structure import basis, request, streamline
from mcutils.surface import CorticalMesh from mcot.surface import CorticalMesh
stop_surfaces = [] stop_surfaces = []
for surf_name, mask_name in zip(args.stop[::2], args.stop[1::2]): for surf_name, mask_name in zip(args.stop[::2], args.stop[1::2]):
......
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
from . import request, utils from . import request, utils
import scipy as sp import scipy as sp
from scipy import linalg from scipy import linalg
from mcutils.surface import grid from mcot.surface import grid
def surface_startpoints(triangles, field_density): def surface_startpoints(triangles, field_density):
......
...@@ -43,7 +43,7 @@ setup(name='gyral_structure', ...@@ -43,7 +43,7 @@ setup(name='gyral_structure',
url='https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure', url='https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure',
packages=find_packages(), packages=find_packages(),
cmdclass={'doc': doc}, cmdclass={'doc': doc},
install_requires=['nibabel', 'scipy', 'mcutils', 'sympy', 'h5py', 'numexpr'], install_requires=['nibabel', 'scipy', 'mcot.surface', 'sympy', 'h5py', 'numexpr'],
scripts=[ scripts=[
'gyral_structure/scripts/gs_track', 'gyral_structure/scripts/gs_track',
'gyral_structure/scripts/gs_dyad_vol', 'gyral_structure/scripts/gs_dyad_vol',
......
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