resolves #205. Quiet numpy output in scripts, remove...

resolves #205. Quiet numpy output in scripts, remove interpolateDisplacementsOnGrid and add checkSurrounded to interpolatePhiField

README.rst

@@ -66,6 +66,8 @@ Changelog
 +-----------------+------------+--------------------------------------------------------------------------------------------------------------------------------------+
 | Version         | Date       | Notes                                                                                                                                |
 +=================+============+======================================================================================================================================+
+| Version 0.6.0.1 | 2021-05-20 | Small fixes to spam-filterPhifield and spam-regularStrain                                                                            |
++-----------------+------------+--------------------------------------------------------------------------------------------------------------------------------------+
 | Version 0.6.0   | 2021-05-04 |  Massive rewrite of image correlation scripts, introduction of spam-pixelSearchPropagate, spam-filterPhiField, spam-passPhiField.    |
 |                 |            |  The spam-pixelSearch is now separate from spam-ldic and spam-ddic, and works both in grid and labelled mode.                        |
 |                 |            |  Please check out new script documentation for a flowchart of how these should be used in series.                                    |

scripts/spam-ITKwatershed

@@ -18,13 +18,13 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-from __future__ import print_function
-
-import tifffile
-import numpy
 import spam.label
 import spam.helpers
 import spam.mesh
+
+import tifffile
+import numpy
+numpy.seterr(all='ignore')
 import scipy.ndimage
 import argparse
 

scripts/spam-ddic

@@ -17,15 +17,17 @@ more details.
 You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
 import spam.DIC
 import spam.label
 import spam.deformation
 import spam.helpers
 
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
+
 import numpy
+numpy.seterr(all='ignore')
 import scipy.ndimage
 import tifffile
 import multiprocessing

scripts/spam-deformImage

@@ -28,13 +28,15 @@ We don't use the more accurate `spam.DIC.deformationFunction.applyPhiField` whic
 
 """
 
-import numpy
-import argparse
 import spam.helpers
 import spam.mesh
 import spam.label
 import spam.DIC
 import spam.deformation
+
+import numpy
+numpy.seterr(all='ignore')
+import argparse
 import tifffile
 
 # Define argument parser object

scripts/spam-discreteStrain

@@ -30,20 +30,21 @@ either projected back to grains (whereby the value at each grain is a weighted l
 ...or projected onto a regular grid.
 """
 
+import spam.helpers
+import spam.DIC
+import spam.deformation
+import spam.mesh
+import spam.label
+
 import os
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 os.environ['OMP_NUM_THREADS'] = '1'
 
 import argparse
 import numpy
+numpy.seterr(all='ignore')
 import multiprocessing
 
-import spam.helpers
-import spam.DIC
-import spam.deformation
-import spam.mesh
-import spam.label
-
 
 # Define argument parser object
 parser = argparse.ArgumentParser(description="spam-discreteStrain "+spam.helpers.optionsParser.GLPv3descriptionHeader +\

scripts/spam-ereg

@@ -18,13 +18,15 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
+import spam.visual.visualClass as visual
+import spam.helpers
+
 import sys
 import os
 from PyQt5.QtWidgets import QApplication, QWidget, QFileDialog, QGridLayout
-import spam.visual.visualClass as visual
 import numpy
+numpy.seterr(all='ignore')
 import tifffile
-import spam.helpers
 
 def main():
     app = QApplication(sys.argv)

scripts/spam-ereg-discrete

@@ -19,14 +19,16 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
+import spam.visual.visualClass as visual
+
 import os
 import sys
 import subprocess
 import spam.helpers
 import spam.label
 import numpy
+numpy.seterr(all='ignore')
 import tifffile
-import spam.visual.visualClass as visual
 import argparse
 
 from PyQt5.QtWidgets import QApplication, QWidget, QFileDialog, QGridLayout, QPushButton

scripts/spam-filterPhiField

@@ -40,16 +40,17 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
-
 import spam.DIC
 import spam.deformation
 import spam.helpers
 #import spam.mesh
 import spam.label
 
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
+
 import numpy
+numpy.seterr(all='ignore')
 import multiprocessing
 import scipy.spatial
 import scipy.ndimage

scripts/spam-gdic

@@ -18,19 +18,20 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import tifffile
-import numpy
-import argparse
-import pickle
-import scipy.ndimage
-
-import spam.datasets
 import spam.mesh
 import spam.DIC
 import spam.deformation
 import spam.label
 import spam.helpers
 
+import numpy
+numpy.seterr(all='ignore')
+import tifffile
+import argparse
+import pickle
+import scipy.ndimage
+
+
 # parser
 import spam.helpers.optionsParser
 parser = argparse.ArgumentParser(description="spam-gdic "+spam.helpers.optionsParser.GLPv3descriptionHeader +\

scripts/spam-imposeBCFromDVC

@@ -20,13 +20,12 @@ this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
 
+import spam.mesh
+import spam.helpers
 
-from __future__ import print_function
 import tifffile
 import numpy
-
-import spam.mesh
-import spam.helpers
+numpy.seterr(all='ignore')
 import argparse
 
 # Define argument parser object

scripts/spam-ldic

@@ -18,15 +18,16 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
-
 import spam.DIC
 import spam.deformation
 import spam.helpers
-import argparse
+
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
 import numpy
+numpy.seterr(all='ignore')
+import argparse
 import scipy.ndimage
 import tifffile
 import multiprocessing

scripts/spam-mmr

@@ -23,6 +23,7 @@ import spam.DIC
 #import pickle
 import tifffile
 import numpy
+numpy.seterr(all='ignore')
 # import scipy.ndimage
 
 import argparse

scripts/spam-moveLabels

@@ -23,6 +23,7 @@ import spam.label as ltk
 import spam.DIC
 import spam.deformation
 import numpy
+numpy.seterr(all='ignore')
 import sys, os
 import tifffile
 #import matplotlib.pyplot as plt

scripts/spam-passPhiField

@@ -55,16 +55,17 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
-
 import spam.DIC
 import spam.deformation
 import spam.helpers
 #import spam.mesh
 import spam.label
 
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
+
 import numpy
+numpy.seterr(all='ignore')
 import multiprocessing
 import scipy.spatial
 import progressbar
@@ -251,6 +252,7 @@ else:
                                                       nNeighbours=args.NUMBER_OF_NEIGHBOURS,
                                                       neighbourRadius=args.NEIGHBOUR_RADIUS,
                                                       interpolateF=args.APPLY_F,
+                                                      checkPointSurrounded=args.CHECK_POINT_SURROUNDED,
                                                       nProcesses=args.PROCESSES,
                                                       verbose=True)
 

scripts/spam-pixelSearch

@@ -22,8 +22,6 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
 import spam.DIC
 import spam.deformation
@@ -31,7 +29,11 @@ import spam.helpers
 #import spam.mesh
 import spam.label
 
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
+
 import numpy
+numpy.seterr(all='ignore')
 import multiprocessing
 import progressbar
 import argparse

scripts/spam-pixelSearchPropagate

@@ -22,14 +22,16 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-import os
-os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
 import spam.DIC
 import spam.mesh
 import spam.helpers
 
+import os
+os.environ['OPENBLAS_NUM_THREADS'] = '1'
+
 import numpy
+numpy.seterr(all='ignore')
 import progressbar
 import argparse
 import tifffile

scripts/spam-reg

@@ -25,11 +25,14 @@ This script is a good initial starting point for a the measurement of a displace
 field, if there is a homogeneous background movement to measure
 """
 
-import numpy
-import argparse
 import spam.helpers
 import spam.DIC
 import spam.deformation
+
+import numpy
+numpy.seterr(all='ignore')
+
+import argparse
 import tifffile
 import os
 

scripts/spam-regularStrain

@@ -18,6 +18,11 @@ You should have received a copy of the GNU General Public License along with
 this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
+import spam.helpers
+import spam.DIC
+import spam.deformation
+import spam.mesh
+
 import os
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 os.environ['OMP_NUM_THREADS'] = '1'
@@ -28,10 +33,6 @@ import multiprocessing
 import numpy
 numpy.seterr(all='ignore')
 
-import spam.helpers
-import spam.DIC
-import spam.deformation
-import spam.mesh
 
 
 # Define argument parser object

setup.py

@@ -99,7 +99,7 @@ name = 'spam'
 description = 'Software for the Practical Analysis of Materials'
 long_description = readReadMe('README.rst')
 long_description_content_type = 'text/x-rst'
-version = '0.6.0.0'
+version = '0.6.0.1'
 author = 'SPAM authors'
 author_email = 'edward.ando@3sr-grenoble.fr'
 copyright = 'SPAM authors 2020'

tools/DIC/deform.py

@@ -23,7 +23,7 @@ import scipy.ndimage
 ###########################################################
 # Take an Phi and apply it (C++) to an image
 ###########################################################
-def applyPhi(im, Phi=None, PhiPoint=None, interpolationOrder=1):
+def applyPhi(im, Phi=None, PhiCentre=None, interpolationOrder=1):
     """
     Deform a 3D image using a deformation function "Phi", applied using spam's C++ interpolator.
     Only interpolation order = 1 is implemented.
@@ -37,7 +37,7 @@ def applyPhi(im, Phi=None, PhiPoint=None, interpolationOrder=1):
             "Phi" deformation function.
             Highly recommended additional argument (why are you calling this function otherwise?)
 
-        PhiPoint : 3x1 array of floats, optional
+        PhiCentre : 3x1 array of floats, optional
             Centre of application of Phi.
             Default = (numpy.array(im1.shape)-1)/2.0
             i.e., the centre of the image
@@ -70,21 +70,21 @@ def applyPhi(im, Phi=None, PhiPoint=None, interpolationOrder=1):
             # print( "\tapplyPhi(): Can't inverse Phi, setting it to identity matrix. Phi is:\n{}".format( Phi ) )
             PhiInv = numpy.eye(4, dtype='<f4')
 
-    if PhiPoint is None:
-        PhiPoint = (numpy.array(im.shape) - 1) / 2.0
+    if PhiCentre is None:
+        PhiCentre = (numpy.array(im.shape) - 1) / 2.0
 
     if interpolationOrder > 1:
         print("DIC.deformationFunction.applyPhi(): interpolation Order > 1 not implemented")
         return
 
     im = im.astype('<f4')
-    PhiPoint = numpy.array(PhiPoint).astype('<f4')
+    PhiCentre = numpy.array(PhiCentre).astype('<f4')
     # We need to inverse Phi for question of direction
     imDef = numpy.zeros_like(im, dtype='<f4')
     DICToolkit.applyPhi(im.astype('<f4'),
                         imDef,
                         PhiInv.astype('<f4'),
-                        PhiPoint.astype('<f4'),
+                        PhiCentre.astype('<f4'),
                         int(interpolationOrder))
 
     return imDef
@@ -92,7 +92,7 @@ def applyPhi(im, Phi=None, PhiPoint=None, interpolationOrder=1):
 ###########################################################
 # Take an Phi and apply it to an image
 ###########################################################
-def applyPhiPython(im, Phi=None, PhiPoint=None, interpolationOrder=3):
+def applyPhiPython(im, Phi=None, PhiCentre=None, interpolationOrder=3):
     """
     Deform a 3D image using a deformation function "Phi", applied using scipy.ndimage.map_coordinates
     Can have orders > 1 but is hungry in memory.
@@ -106,7 +106,7 @@ def applyPhiPython(im, Phi=None, PhiPoint=None, interpolationOrder=3):
             "Phi" linear deformation function.
             Highly recommended additional argument (why are you calling this function otherwise?)
 
-        PhiPoint : 3x1 array of floats, optional
+        PhiCentre : 3x1 array of floats, optional
             Centre of application of Phi.
             Default = (numpy.array(im1.shape)-1)/2.0
             i.e., the centre of the image
@@ -130,8 +130,8 @@ def applyPhiPython(im, Phi=None, PhiPoint=None, interpolationOrder=3):
             # print( "\tapplyPhiPython(): Can't inverse Phi, setting it to identity matrix. Phi is:\n{}".format( Phi ) )
             PhiInv = numpy.eye(4)
 
-    if PhiPoint is None:
-        PhiPoint = (numpy.array(im.shape) - 1) / 2.0
+    if PhiCentre is None:
+        PhiCentre = (numpy.array(im.shape) - 1) / 2.0
 
     imDef = numpy.zeros_like(im, dtype='<f4')
 
@@ -142,16 +142,16 @@ def applyPhiPython(im, Phi=None, PhiPoint=None, interpolationOrder=3):
                                     0:im.shape[2]]
 
     # Copy into coordinatesInitial
-    coordinatesInitial[0, :] = coordinates_mgrid[0].ravel() - PhiPoint[0]
-    coordinatesInitial[1, :] = coordinates_mgrid[1].ravel() - PhiPoint[1]
-    coordinatesInitial[2, :] = coordinates_mgrid[2].ravel() - PhiPoint[2]
+    coordinatesInitial[0, :] = coordinates_mgrid[0].ravel() - PhiCentre[0]
+    coordinatesInitial[1, :] = coordinates_mgrid[1].ravel() - PhiCentre[1]
+    coordinatesInitial[2, :] = coordinates_mgrid[2].ravel() - PhiCentre[2]
 
     # Apply Phi to coordinates
     coordinatesDef = numpy.dot(PhiInv, coordinatesInitial)
 
-    coordinatesDef[0, :] += PhiPoint[0]
-    coordinatesDef[1, :] += PhiPoint[1]
-    coordinatesDef[2, :] += PhiPoint[2]
+    coordinatesDef[0, :] += PhiCentre[0]
+    coordinatesDef[1, :] += PhiCentre[1]
+    coordinatesDef[2, :] += PhiCentre[2]
 
     imDef += scipy.ndimage.map_coordinates(im,
                                            coordinatesDef[0:3],