removed uses of arraydata() (#93) + some cleaning

pyaims/bin/AimsCiftiSubMatrix.py

@@ -83,19 +83,19 @@ def main():
                   if gyrus in labels_inv_map[i]]
         if len(gyrdef) != 0:
             tex, gyrus_num = gyrdef[0]
-            gyrus_indices = np.where(gyri[tex][0].arraydata() == gyrus_num)[0]
+            gyrus_indices = np.where(gyri[tex][0].np == gyrus_num)[0]
             gyri_vert_l.append((tex, gyrus_indices))
         else:
             try:
                 gyrus_num = int(gyrus)
             except ValueError:
                 print("Gyrus %s not found" % gyrus)
                 continue
-            texs = [gyrus_num in roi[0].arraydata() for roi in gyri]
+            texs = [gyrus_num in roi[0].np for roi in gyri]
             for tex in len(texs):
                 if texs[tex]:
                     gyrus_indices = np.where(
-                        gyri[tex][0].arraydata() == gyrus_num)[0]
+                        gyri[tex][0].np == gyrus_num)[0]
                     gyri_vert_l.append((tex, gyrus_indices))
 
     # concatenate by texture/surface
@@ -115,7 +115,7 @@ def main():
     print('row_indices:', len(row_indices))
     total_vertices = sum([len(troi[i][0]) for i in range(len(troi))])
     print('total_vertices:', total_vertices)
-    col_vertices = [(i, np.where(troi[i][0].arraydata() != 0)[0])
+    col_vertices = [(i, np.where(troi[i][0].np != 0)[0])
                     for i in range(len(troi))]
     col_indices = np.hstack([c.getIndicesForSurfaceIndices(1, i, vert)
                               for i, vert in col_vertices])
@@ -134,7 +134,7 @@ def main():
         print('row:', row, ':', i, '/', len(row_indices), 'dense:',
               gyr_mat.isDense())
         mat.readRow(row)
-        row_data = mat.getRow(row).arraydata()
+        row_data = mat.getRow(row).np
         #row_data[np.isnan(row_data)] = 0
         row_data[np.isinf(row_data)] = 0
         mat.freeRow(row)

pyaims/python/soma/aims/meshSplit.py

@@ -93,7 +93,7 @@ def meshSplit2(mesh, tex, graph, voxel_size=None, tex_time_step=None):
     else:
         tex_tstep = tex
     # labels in the texture
-    labels = (numpy.unique(tex_tstep[0].arraydata())).tolist()
+    labels = (numpy.unique(tex_tstep[0].np)).tolist()
     #if 0 in labels:
         #labels.remove(0)
 

pyaims/python/soma/aims/texturetools.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-
 from soma import aims, aimsalgo
 from soma.utils.csv_utils import dict_to_table
 import numpy
@@ -17,9 +16,9 @@ def mergeLabelsFromTexture(tex, labels_list, new_label):
           otex: labeled texture with merged regions
     """
     otex = aims.TimeTexture_S16()
-    tex_ar = tex[0].arraydata()
+    tex_ar = tex[0].np
     otex[0].assign(tex_ar)
-    otex_ar = otex[0].arraydata()
+    otex_ar = otex[0].np
     for i in labels_list:
         otex_ar[otex_ar == int(i)] = new_label
     return otex
@@ -37,8 +36,8 @@ def extractLabelsFromTexture(tex, labels_list, new_label):
     otex[0].reserve(tex[0].nItem())
     for i in range(tex[0].nItem()):
         otex[0].push_back(0)
-    tex_ar = tex[0].arraydata()
-    otex_ar = otex[0].arraydata()
+    tex_ar = tex[0].np
+    otex_ar = otex[0].np
     for i in labels_list:
         otex_ar[tex_ar == int(i)] = new_label
     return otex
@@ -69,7 +68,7 @@ def connectedComponents(mesh, tex, areas_mode=0):
         with area = 16.5 and 6.0 respectively, areas are in square mm
     """
     # create a numpy array from aims object
-    dtex = tex[0].arraydata()
+    dtex = tex[0].np
 
     # number of vertices
     nbvert = len(mesh.vertex())
@@ -97,7 +96,7 @@ def connectedComponents(mesh, tex, areas_mode=0):
         otex[0].assign((dtex == label))
         label_cc = aimsalgo.AimsMeshLabelConnectedComponent(mesh, otex, 0, 0)
         # transform aims.TimeTexture_S16 to numpy array
-        label_cc_np = label_cc[0].arraydata()
+        label_cc_np = label_cc[0].np
         step_cc[label-1].assign(label_cc_np)
 
         if areas_mode:
@@ -130,19 +129,19 @@ def remove_non_principal_connected_components(mesh, tex, trash_label):
     -------
     out_tex: label texture
     """
-    t0 = tex[0].arraydata()
+    t0 = tex[0].np
     t0 += 1  # 0 is a real label
     conn_comp, areas = connectedComponents(mesh, tex, areas_mode=True)
     t0 -= 1
-    dtype = tex[0].arraydata().dtype
+    dtype = tex[0].np.dtype
     out_tex = aims.TimeTexture(dtype=dtype)
     out_tex[0].assign(numpy.zeros(tex[0].size(), dtype=dtype))
-    out_arr = out_tex[0].arraydata()
+    out_arr = out_tex[0].np
     out_arr[:] = trash_label
     for label in conn_comp.keys():
         comps = conn_comp[label]
         largest = numpy.argmax(areas[label + 1]) + 1
-        comp_arr = comps.arraydata()
+        comp_arr = comps.np
         out_arr[comp_arr==largest] = label
     return out_tex
 
@@ -156,8 +155,8 @@ def meshDiceIndex(mesh, texture1, texture2, timestep1=0,
 
     return
     """
-    tex1 = texture1[timestep1].arraydata()
-    tex2 = texture2[timestep2].arraydata()
+    tex1 = texture1[timestep1].np
+    tex2 = texture2[timestep2].np
     if labels_table1 is not None:
         tex1 = numpy.array([labels_table1[x] for x in tex1])
     if labels_table2 is not None:
@@ -204,7 +203,7 @@ def average_texture(output, inputs):
     for fname in inputs:
         tex.append(aims.read(fname))
     # make a 2D array from a series of textures
-    ar = numpy.vstack([t[0].arraydata() for t in tex])
+    ar = numpy.vstack([t[0].np for t in tex])
     # replace the negative values by positive integers
     if len(ar[ar == -1]) != 0:
         tmp_label = numpy.max(ar) + 1
@@ -284,17 +283,17 @@ def vertex_texture_to_polygon_texture(mesh, tex, allow_cut=False):
       * new mesh with possibly split triangles
     It only works for meshes of triangles.
     """
-    dtype = tex[list(tex.keys())[0]].arraydata().dtype
+    dtype = tex[list(tex.keys())[0]].np.dtype
     poly_tex = aims.TimeTexture(dtype=dtype)
 
     if allow_cut:
         out_mesh = mesh.__class__(mesh)
 
     for t, tex0 in tex.items():
-        tdata = tex0.arraydata()
+        tdata = tex0.np
         ptex0 = poly_tex[t]
         ptex0.resize(len(mesh.polygon(t)))
-        poly_labels = ptex0.arraydata()
+        poly_labels = ptex0.np
         if allow_cut:
             added_vert = {}
             vertex = out_mesh.vertex(t)
@@ -395,7 +394,7 @@ def mesh_to_polygon_textured_mesh(mesh, poly_tex):
     """
     out_mesh = mesh.__class__()
     out_tex = poly_tex.__class__()
-    dtype = poly_tex[list(poly_tex.keys())[0]].arraydata().dtype
+    dtype = poly_tex[list(poly_tex.keys())[0]].np.dtype
     for t, tex0 in poly_tex.items():
         print('t:', t)
         overt = out_mesh.vertex(t)
@@ -406,8 +405,8 @@ def mesh_to_polygon_textured_mesh(mesh, poly_tex):
         opoly.assign(mesh.polygon())
         otex = out_tex[t]
         otex.assign(numpy.zeros(mesh.vertex().size(), dtype=dtype) - 1)
-        #otex_arr = otex.arraydata()
-        tex_arr = tex0.arraydata()
+        #otex_arr = otex.np
+        tex_arr = tex0.np
         added = {}
         for p in range(len(mesh.polygon())):
             plabel = tex_arr[p]
@@ -427,7 +426,7 @@ def mesh_to_polygon_textured_mesh(mesh, poly_tex):
                         poly[i] = vb
                         otex.data().append(plabel)
                         added[(v, plabel)] = vb
-                        #otex_arr = otex.arraydata()
+                        #otex_arr = otex.np
 
     out_mesh.updateNormals()
     return out_mesh, out_tex
@@ -529,7 +528,7 @@ def clean_gyri_texture(mesh, gyri_tex):
         if areas_measures[label].size != 1:
             wrong_labels.append(label)
     for label in wrong_labels:
-        cc_tex_label = cc_tex[label - 1].arraydata()
+        cc_tex_label = cc_tex[label - 1].np
         areas_measures_cc = areas_measures[label]
         cc_nb = areas_measures_cc.size
         for l in range(1, cc_nb):

pyaimsalgo/python/soma/aimsalgo/mesh_coordinates_sphere_resampling.py

@@ -9,10 +9,7 @@
 # and INRIA at the following URL "http://www.cecill.info".
 ############################################################################
 
-from __future__ import print_function
-
 # system import
-from __future__ import absolute_import
 import numpy
 
 # Soma import
@@ -41,8 +38,8 @@ def draw_sphere(mesh, longitude, latitude):
         a spherical triangulation of the subject of its cortical hemisphere,
         projected on a sphere
     """
-    lon = longitude[0].arraydata()
-    lat = latitude[0].arraydata()
+    lon = longitude[0].np
+    lat = latitude[0].np
 
     nmesh = numpy.asarray(mesh.vertex())
 
@@ -162,8 +159,8 @@ def resample_mesh_to_sphere(
 
     #  ...
     # multiply latitudes by 2 to get same amplitude on both coords
-    latitude = aims.TimeTexture(latitude[0].arraydata() * 2)
-    slat_tex = aims.TimeTexture(slat_tex[0].arraydata() * 2)
+    latitude = aims.TimeTexture(latitude[0].np * 2)
+    slat_tex = aims.TimeTexture(slat_tex[0].np * 2)
     interpoler = aims.CoordinatesFieldMeshInterpoler(
         mesh, sphere, latitude, longitude, slat_tex, slon_tex)
 
@@ -223,8 +220,8 @@ def resample_texture_to_sphere(
 
     #  ...
     # multiply latitudes by 2 to get same amplitude on both coords
-    latitude = aims.TimeTexture(latitude[0].arraydata() * 2)
-    slat_tex = aims.TimeTexture(slat_tex[0].arraydata() * 2)
+    latitude = aims.TimeTexture(latitude[0].np * 2)
+    slat_tex = aims.TimeTexture(slat_tex[0].np * 2)
     interpoler = aims.CoordinatesFieldMeshInterpoler(
         mesh, sphere, latitude, longitude, slat_tex, slon_tex)
 
@@ -370,8 +367,8 @@ def refine_sphere_mesh(init_sphere, avg_dist_texture, current_sphere,
                             - init_sphere.vertex()[
                             init_sphere.polygon()[0][0]]).norm()
 
-    init_lat = aims.TimeTexture(init_lat[0].arraydata() * 2)
-    current_lat = aims.TimeTexture(current_lat[0].arraydata() * 2)
+    init_lat = aims.TimeTexture(init_lat[0].np * 2)
+    current_lat = aims.TimeTexture(current_lat[0].np * 2)
     interpoler = aims.CoordinatesFieldMeshInterpoler(init_sphere,
                                                      current_sphere,
                                                      init_lat,

pyaimsalgo/python/soma/aimsalgo/meshwatershedtools.py

@@ -19,20 +19,17 @@
 """
 
 
-#----------------------------Imports-------------------------------------------
+# ----------------------------Imports------------------------------------------
 
 
 # import system
-from __future__ import absolute_import
-from __future__ import print_function
 import numpy
-import sys
 
 # soma import
 from soma import aims, aimsalgo
 from six.moves import range
 
-#----------------------------Functions-----------------------------------------
+# ---------------------------Functions-----------------------------------------
 
 
 def _clean_after_merge(labels, parents, valid):
@@ -160,10 +157,10 @@ def watershedWithBasinsMerging(
     # labelWt: array of shape (number of vertices)
     #          labelling of the vertices according to their basin
 
-    data = tex[0].arraydata()
-    idxW = idxWt[0].data().arraydata()
-    majorW = majorWt[0].data().arraydata()
-    labelW = labelWt[0].data().arraydata()
+    data = tex[0].np
+    idxW = idxWt[0].data().np
+    majorW = majorWt[0].data().np
+    labelW = labelWt[0].data().np
 
     if size_min != 0 or depth_min != 0:
         size = numpy.asarray([len(numpy.where(labelW == x)[0])
@@ -173,7 +170,7 @@ def watershedWithBasinsMerging(
         # Blobs
         blobindices = aimsalgo.blobsHeights(
             mesh, tex[0].data(), labelWt[0].data())
-        blobheights = data[blobindices.arraydata()]
+        blobheights = data[blobindices.np]
         blobdepths = data[idxW] - blobheights
         print("criteria depth: ", blobdepths)
 

pyaimsalgo/python/soma/wip/aimsalgo/foldsgraphthickness.py

@@ -32,14 +32,11 @@
 # The fact that you are presently reading this means that you have had
 # knowledge of the CeCILL-B license and that you accept its terms.
 
-from __future__ import print_function
-from __future__ import absolute_import
 from soma import aims
-from soma import aimsalgo
 import numpy
 
 
-class FoldsGraphThickness(object):
+class FoldsGraphThickness:
     def __init__(self, fold_graph, lgw_vol, gm_wm_mesh, gm_lcr_mesh,
                  voronoi=None):
         self.fold_graph = fold_graph
@@ -89,7 +86,7 @@ def printbucket(bck, vol, value):
             f1.doit(seed, [-self.LCR_label, -self.GM_label], seed_label_list)
             self.voronoi_vol = f1.voronoiVol()
             print("Voronoi in White matter")
-            n = numpy.array(voronoi_vol, copy=False)
+            n = self.voronoi_vol.np
             n[n == -1] = -100  # avoid value -1 which doesn't seem to work (!)
             del n
             f1.doit(self.voronoi_vol, [-100], seed_label_list)
@@ -127,23 +124,21 @@ def vorTexCreation(mesh):
     def graphProcess(self):
         voxel_size = self.lgw_vol.header()["voxel_size"]
         voxel_volume = voxel_size[0]*voxel_size[1]*voxel_size[2]
-        coords = self.mid_interface.arraydata() != -1
-        data = self.mid_interface.arraydata()[coords]
+        coords = self.mid_interface.np != -1
+        data = self.mid_interface[coords]
         self.fold_graph['thickness_mean'] = data.mean()
         self.fold_graph['thickness_std'] = data.std()
-        coords = self.lgw_vol.arraydata() == self.GM_label
+        coords = self.lgw_vol.np == self.GM_label
         GM_voxels = numpy.where(coords)[0].size
         self.fold_graph['GM_volume'] = GM_voxels * voxel_volume
-        coords = self.lgw_vol.arraydata() == self.LCR_label
+        coords = self.lgw_vol.np == self.LCR_label
         LCR_voxels = numpy.where(coords)[0].size
         self.fold_graph['LCR_volume'] = LCR_voxels * voxel_volume
         self.fold_graph['CSF_volume'] = LCR_voxels * voxel_volume
 
     def vertexProcess(self):
         print("vertexProcess")
         voxel_size = self.lgw_vol.header()["voxel_size"]
-        voxel_volume = voxel_size[0]*voxel_size[1]*voxel_size[2]
-        coords = self.mid_interface.arraydata() != -1
 
         def vertex_mesh(self, v, skel):
             cut_mesh = aims.SurfaceManip.meshExtract(
@@ -168,8 +163,8 @@ def vertex_mesh(self, v, skel):
         for v in self.fold_graph.vertices():
             try:
                 skel = v['skeleton_label']
-                print("skel : " + str(skel) + " compteur : " + str(compteur) + '/'
-                      + str(n))
+                print("skel : " + str(skel) + " compteur : " + str(compteur)
+                      + '/' + str(n))
                 compteur = compteur + 1
                 vertex_mesh(self, v, skel)
             except: