Replace mcutils with mcot

.gitlab-ci.yml

@@ -2,7 +2,6 @@ before_script:
   - apt-get update -qq
   - apt-get install python3
   - pip install numpy pandas seaborn
-  - pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/mcutils.git
   - pip install .
   - pip install pytest
 

README.md

@@ -11,7 +11,6 @@ Installation
 The requirements can be installed using conda and pip:
 ```sh
 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
 ```
 

doc/tutorial.rst

@@ -7,7 +7,6 @@ Gyral structure can be installed using pip:
 
 .. 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
 
 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:
     import nibabel as nib
     import numpy as np
     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
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

gyral_structure/qc/surface.py

@@ -2,7 +2,7 @@
 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.basis import BasisFunc
 from nibabel import cifti2

gyral_structure/request.py

@@ -16,7 +16,7 @@ in multiple cost functions.
 import scipy as sp
 import itertools
 from itertools import zip_longest
-from mcutils.surface import CorticalMesh
+from mcot.surface import CorticalMesh
 import nibabel
 import os
 from numpy import linalg

gyral_structure/scripts/gs_deform_surface

@@ -20,8 +20,8 @@ args = parser.parse_args()
 import nibabel
 import numpy as np
 from gyral_structure import basis, streamline
-from mcutils.surface import CorticalMesh, grid
-from mcutils.utils.write_gifti import write_gifti
+from mcot.surface import CorticalMesh, grid
+from mcot.surface import write_gifti
 from numpy import linalg
 from scipy import ndimage
 

gyral_structure/scripts/gs_dyad_surf

@@ -10,9 +10,9 @@ args = parser.parse_args()
 
 import nibabel
 from gyral_structure import basis, request, utils
-from mcutils.surface import CorticalMesh
+from mcot.surface import CorticalMesh
 import scipy as sp
-import cifti
+from nibabel import cifti2
 
 basis_func, best_fit_arr = basis.read(args.field)
 img = nibabel.load(args.surface)
@@ -34,6 +34,6 @@ for idx in range(arr_triangle.shape[0]):
     conn, val = sp.broadcast_arrays(surf.faces, arr_triangle[idx][None, :])
     nconn = sp.bincount(conn.flatten(), minlength=surf.nvertices)
     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'])
-cifti.write(args.output, arr_vertices, (cifti.Scalar.from_names(['density (crossing)', 'density (total)', 'radiality', 'x', 'y', 'z']), bm))
+bm = cifti2.BrainModelAxis.from_mask(mask, name=img.darrays[0].metadata['AnatomicalStructurePrimary'])
+cifti2.Cifti2Image(arr_vertices, (cifti2.ScalarAxis(['density (crossing)', 'density (total)', 'radiality', 'x', 'y', 'z']), bm)).to_filename(args.output)
 

gyral_structure/scripts/gs_fit

@@ -41,7 +41,7 @@ args = parser.parse_args()
 import nibabel as nib
 import numpy as np
 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 nibabel import affines
 

gyral_structure/scripts/gs_mask

@@ -25,7 +25,7 @@ parser.add_argument("-N", "--norient", default=300, type=int,
                          "default: 300")
 args = parser.parse_args()
 
-from mcutils.surface import CorticalMesh, grid, orientation
+from mcot.surface import CorticalMesh, grid, orientation
 import nibabel as nib
 import numpy as np
 from scipy import ndimage

gyral_structure/scripts/gs_qc

@@ -24,7 +24,7 @@ parser.add_argument("-sp", "--skip_plots", action='store_true',
 args = parser.parse_args()
 
 from gyral_structure.basis import read
-from mcutils.surface import CorticalMesh, Cortex
+from mcot.surface import CorticalMesh, Cortex
 import os
 from gyral_structure import qc
 import nibabel as nib

gyral_structure/scripts/gs_track

@@ -17,7 +17,7 @@ if len(args.stop) % 2 != 0:
 import nibabel
 from numpy import linalg
 from gyral_structure import basis, request, streamline
-from mcutils.surface import CorticalMesh
+from mcot.surface import CorticalMesh
 
 stop_surfaces = []
 for surf_name, mask_name in zip(args.stop[::2], args.stop[1::2]):

gyral_structure/streamline.py

@@ -3,7 +3,7 @@
 from . import request, utils
 import scipy as sp
 from scipy import linalg
-from mcutils.surface import grid
+from mcot.surface import grid
 
 
 def surface_startpoints(triangles, field_density):

setup.py

@@ -43,7 +43,7 @@ setup(name='gyral_structure',
       url='https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure',
       packages=find_packages(),
       cmdclass={'doc': doc},
-      install_requires=['nibabel', 'scipy', 'mcutils', 'sympy', 'h5py', 'numexpr'],
+      install_requires=['nibabel', 'scipy', 'mcot.surface', 'sympy', 'h5py', 'numexpr'],
       scripts=[
           'gyral_structure/scripts/gs_track',
           'gyral_structure/scripts/gs_dyad_vol',