Fix time series writer (tiff->vtk)

install.bash

@@ -20,7 +20,8 @@ fi
 if [ "$1" == "coverage" ]
 then
     python setup.py install
-    coverage run setup.py test
+    coverage run -m pytest
+    coverage combine && coverage report
     coverage html
 fi
 

requirements-3.6.txt

-# If you're changing this, consider relaunching:
-# https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/docker-ttk/-/pipelines
-
-numpy==1.19.5 # Python >=3.6
-
-scipy==1.5.4 # Python >=3.6
-
-scikit-image==0.17.2 # Python >=3.6
-
-tifffile==2020.8.25 # Python >=3.6
-
-matplotlib==3.3.4 # Python >=3.6
-
-SimpleITK==2.0.2
-
-progressbar==2.5
-
-gmsh==4.8.0
-meshio==4.3.11 # Python >=3.6
-
-# Anything later than this causes an abort at the end of sphinx 3.5.2 build
-pybind11==2.5.0 # Python !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, >=2.7
-
-# multigrid solver for random walker segmentation
-pyamg==4.0.0
-
-############
-# Optional #
-############
-
-# mpi
-# mpi4py==3.0.3
-
-# Jupyter
-#ipykernel==5.5.0 # Python >=3.5
-ipython==7.16.1 # Python >=3.6
-
-# R (correlated random field)
-rpy2==3.2.2
-
-#############
-# Graphical #
-#############
-#PyQt5==5.15.4 # Python >=3.6
-#PyQt5-sip==12.8.1 # Python >=3.5
-#qimage2ndarray==1.8.3

requirements-3.7.txt

@@ -17,6 +17,7 @@ progressbar==2.5
 
 gmsh==4.8.0
 meshio==4.3.11 # Python >=3.6
+h5py==3.2.1 # Python >=3.7
 
 # Anything later than this causes an abort at the end of sphinx 3.5.2 build
 pybind11==2.5.0 # Python !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, >=2.7

requirements.txt

@@ -17,6 +17,7 @@ progressbar==2.5
 
 gmsh==4.8.0
 meshio==4.3.11 # Python >=3.6
+h5py==3.1.0 # Python >=3.6
 
 # Anything later than this causes an abort at the end of sphinx 3.5.2 build
 pybind11==2.5.0 # Python !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, >=2.7

tools/helpers/vtkio.py

@@ -528,8 +528,8 @@ def TIFFtoVTK(fileName, voxelSize=1.0):
     if len(fileName) == 1:
         meshio.write_points_cells(f"{f}.vtk", points, {"hexahedron": cells}, cell_data={"grey": [im.T.ravel()]})
     else:
-        writer = meshio.XdmfTimeSeriesWriter(f"{f}.xmf")
-        writer.write_points_cells(points, {"hexahedron": cells})
+        with meshio.xdmf.TimeSeriesWriter(f"{f}.xmf") as writer:
+            writer.write_points_cells(points, [("hexahedron", cells)])
             for i, name in enumerate(fileName):
                 im = tifffile.imread(name)
                 writer.write_data(i, cell_data={"grey": [im.T.ravel()]})

tools/tests/test_vtkio.py

 # -*- coding: utf-8 -*-
-from __future__ import print_function
-
 import unittest
 import numpy
 import os
@@ -15,11 +13,12 @@ class testAll(unittest.TestCase):
         try:
             # pass
             os.remove("./spam.vtk")
-            os.remove("./tmpsnow.tif")
-            os.remove("./tmpsnow.vtk")
-            #os.remove("tools/data/snow/snow.vtk")
-            #os.remove("tools/data/snow/snow.h5")
-            #os.remove("tools/data/snow/snow.xmf")
+            os.remove("./snow-1.tif")
+            os.remove("./snow-2.tif")
+            os.remove("./snow-3.tif")
+            os.remove("./snow-1.vtk")
+            os.remove("./snow-1.h5")
+            os.remove("./snow-1.xmf")
         except OSError:
             pass
 
@@ -64,6 +63,10 @@ class testAll(unittest.TestCase):
         tensor = numpy.random.rand(4, 5, 6, 3, 3)
         spam.helpers.writeStructuredVTK(pointData={'c': tensor})
 
+        # write field with wrong format
+        dummy = numpy.random.rand(4, 5, 6, 3, 2)
+        spam.helpers.writeStructuredVTK(pointData={'d': dummy})
+
         # write 2 point and 2 cell
         cellScalars = numpy.random.rand(4, 5, 6)
         cellVectors = numpy.random.rand(4, 5, 6, 3)
@@ -129,13 +132,19 @@ class testAll(unittest.TestCase):
         spam.helpers.writeGlyphsVTK(coordinates, pointData)
 
     def test_TIFFtoVTK(self):
-        im = spam.datasets.loadSnow()[0:20, 0:20, 0:20]
         # Make it smaller because this takes a long time
+        im1 = spam.datasets.loadSnow()[0:20, 0:20, 0:20]
+        im2 = spam.datasets.loadSnow()[0:20, 0:20, 2:22]
+        im3 = spam.datasets.loadSnow()[0:20, 0:20, 4:24]
+
         import tifffile
-        tifffile.imsave("./tmpsnow.tif", im)
-        spam.helpers.TIFFtoVTK("./tmpsnow.tif")
+        tifffile.imsave("./snow-1.tif", im1)
+        tifffile.imsave("./snow-2.tif", im2)
+        tifffile.imsave("./snow-3.tif", im3)
+
+        spam.helpers.TIFFtoVTK("./snow-1.tif")
         # VTK = spam.helpers.readStructuredVTK("tmpsnow.vtk")  # can't read binary
-        # spam.helpers.TIFFtoVTK(["tmpsnow.tif", "tmpsnow.tif"])
+        spam.helpers.TIFFtoVTK(["snow-1.tif", "snow-2.tif", "snow-3.tif"])