Merge pull request #72 from abel-research/aopReadWrite

Aop read write

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -51,4 +51,11 @@ tests/obj.obj
 tests/stl_file_2_hc.stl
 tests/stl_file_2_lp.stl
 tests/stl_file_trim.stl
-tests/reg_test*
+tests/Example_write.aop
+tests/aop_test.stl
+tests/aop_write.aop
+tests/aop_write_2.aop
+
+tests/reg_test*
+
+dev.py

ampscan/analyse/__init__.py

@@ -1,5 +1,5 @@
 from .analyse import (calc_volume_closed, create_slices, calc_perimeter, calc_widths, calc_csa, est_volume, 
-                      visualise_slices, plot_slices, MeasurementsOut, CMapOut)
+                      visualise_slices, plot_slices, MeasurementsOut, CMapOut, logEuPath)
 from .output import getPDF, generateRegBinsCsv, generateRegCsv, generate_spec
 
 del analyse, output

ampscan/analyse/analyse.py

@@ -6,7 +6,6 @@
 """
 
 import numpy as np
-from ampscan.core import AmpObject
 import matplotlib.pyplot as plt
 import matplotlib.colors as clr
 import matplotlib.colorbar as clb
@@ -40,29 +39,7 @@ def calc_volume_closed(amp_in, return_closed=False):
     amp: AmpObject
         If return_closed is True, then the closed shape is returned 
     """
-    amp = AmpObject({
-        'vert': amp_in.vert.copy(),
-        'faces': amp_in.faces.copy(),
-        'values': amp_in.values.copy(),
-    })
-    amp.calcStruct()
-    # Fill in the holes
-    while (amp.faceEdges == -99999).sum() != 0: 
-        # Find the edges which are only conected to one face
-        edges = (amp.faceEdges == -99999).sum(axis=1).astype(bool)
-        edges = amp.edges[edges, :]
-        # Return the vert indicies for the loop
-        vInd = logEuPath(edges)
-        # Calculate the mmidpoint 
-        midpoint = amp.vert[vInd, :].mean(axis=0)
-        # Add in the new vertex
-        amp.vert = np.r_[amp.vert, midpoint[None, :]]
-        f0 = amp.vert.shape[0] - 1
-        # Add in each face using adjacent vertices in loop
-        for f1, f2 in zip(vInd, np.roll(vInd, 1)):
-            amp.faces = np.r_[amp.faces, [[f1, f0, f2]]]
-        # Update structure and check if any more holes (algorithm keeps going until all holes filled)
-        amp.calcStruct()
+    amp = amp_in.close()
     # Calculate the area of each face in the array using vector cross product
     v01 = amp.vert[amp.faces[:, 1], :] - amp.vert[amp.faces[:, 0], :]
     v02 = amp.vert[amp.faces[:, 2], :] - amp.vert[amp.faces[:, 0], :]
@@ -77,7 +54,7 @@ def calc_volume_closed(amp_in, return_closed=False):
 
 
 
-def create_slices(amp, *args,  typ='slices', axis = 2):
+def create_slices(amp, *args,  typ='slices', axis = 2, order=True):
     r"""
     Generate polygons from planar slices through the AmpObject. The slices are either defined as a 
     list of positions in some axis
@@ -142,7 +119,7 @@ def create_slices(amp, *args,  typ='slices', axis = 2):
     polys = []
     for plane in slices:
         try:
-            ind = vE < plane
+            ind = vE <= plane
             # Select edges with one vertex above and one below the slice plane 
             validEdgeInd = np.where(np.logical_xor(ind[:,0], ind[:,1]))[0]
             validfE = amp.faceEdges[validEdgeInd, :].astype(int)