resqpy 4.5.0__py3-none-any.whl → 4.6.3__py3-none-any.whl
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- resqpy/__init__.py +1 -1
- resqpy/grid/_defined_geometry.py +15 -9
- resqpy/grid_surface/__init__.py +61 -40
- resqpy/grid_surface/_find_faces.py +351 -243
- resqpy/grid_surface/grid_surface_cuda.py +172 -125
- resqpy/lines/_common.py +10 -7
- resqpy/lines/_polyline.py +20 -0
- resqpy/lines/_polyline_set.py +64 -34
- resqpy/model/_hdf5.py +17 -7
- resqpy/model/_model.py +2 -1
- resqpy/model/_xml.py +4 -4
- resqpy/multi_processing/_multiprocessing.py +1 -0
- resqpy/multi_processing/wrappers/grid_surface_mp.py +12 -3
- resqpy/olio/intersection.py +2 -3
- resqpy/olio/read_nexus_fault.py +71 -67
- resqpy/olio/triangulation.py +66 -22
- resqpy/olio/vector_utilities.py +175 -71
- resqpy/olio/wellspec_keywords.py +5 -4
- resqpy/olio/write_hdf5.py +16 -8
- resqpy/olio/xml_et.py +3 -3
- resqpy/property/_collection_get_attributes.py +11 -5
- resqpy/property/_property.py +16 -5
- resqpy/property/property_collection.py +36 -11
- resqpy/surface/__init__.py +2 -2
- resqpy/surface/_surface.py +69 -6
- resqpy/time_series/__init__.py +3 -2
- resqpy/time_series/_time_series.py +10 -0
- {resqpy-4.5.0.dist-info → resqpy-4.6.3.dist-info}/METADATA +3 -3
- {resqpy-4.5.0.dist-info → resqpy-4.6.3.dist-info}/RECORD +31 -31
- {resqpy-4.5.0.dist-info → resqpy-4.6.3.dist-info}/WHEEL +1 -1
- {resqpy-4.5.0.dist-info → resqpy-4.6.3.dist-info}/LICENSE +0 -0
resqpy/lines/_polyline_set.py
CHANGED
@@ -68,7 +68,9 @@ class PolylineSet(rql_c._BasePolyline):
|
|
68
68
|
self.save_polys = False
|
69
69
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self.boolnotconstant = None
|
70
70
|
self.boolvalue = None
|
71
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+
self.closed_array = None
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71
72
|
self.crs_uuid = crs_uuid
|
73
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+
self.indices = None
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72
74
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|
73
75
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super().__init__(model = parent_model,
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74
76
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uuid = uuid,
|
@@ -92,10 +94,11 @@ class PolylineSet(rql_c._BasePolyline):
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92
94
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break
|
93
95
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self.polys = polylines
|
94
96
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# Setting the title of the first polyline given as the PolylineSet title
|
95
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-
if
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96
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-
|
97
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-
|
98
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-
|
97
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+
if not self.title:
|
98
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+
if len(polylines) > 1:
|
99
|
+
self.title = f"{polylines[0].title} + {len(polylines)-1} polylines"
|
100
|
+
else:
|
101
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+
self.title = polylines[0].title
|
99
102
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|
100
103
|
elif irap_file is not None: # Create from an input IRAP file
|
101
104
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if crs_uuid is None:
|
@@ -113,6 +116,7 @@ class PolylineSet(rql_c._BasePolyline):
|
|
113
116
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root = self.root
|
114
117
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|
115
118
|
self.rep_int_root = self.model.referenced_node(rqet.find_tag(root, 'RepresentedInterpretation'))
|
119
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+
self.closed_array = np.empty((0,), dtype = bool)
|
116
120
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|
117
121
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for patch_node in rqet.list_of_tag(root, 'LinePatch'): # Loop over all LinePatches - likely just the one
|
118
122
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assert patch_node is not None # Required field
|
@@ -134,7 +138,7 @@ class PolylineSet(rql_c._BasePolyline):
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134
138
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closed_array = self.get_bool_array(closed_node)
|
135
139
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136
140
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count_node = rqet.find_tag(patch_node, 'NodeCountPerPolyline')
|
137
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-
rql_c.load_hdf5_array(self, count_node, 'count_perpol', tag = 'Values')
|
141
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+
rql_c.load_hdf5_array(self, count_node, 'count_perpol', tag = 'Values', dtype = 'int')
|
138
142
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|
139
143
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points_node = rqet.find_tag(geometry_node, 'Points')
|
140
144
|
assert points_node is not None # Required field
|
@@ -155,12 +159,16 @@ class PolylineSet(rql_c._BasePolyline):
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155
159
|
# delattr(self,'count_perpol')
|
156
160
|
|
157
161
|
self.polys.extend(subpolys)
|
162
|
+
self.closed_array = np.concatenate((self.closed_array, closed_array))
|
163
|
+
|
164
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+
self.bool_array_format()
|
158
165
|
|
159
166
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def _set_from_irap(self, irap_file):
|
160
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inpoints = rsl.read_lines(irap_file)
|
161
168
|
self.count_perpol = []
|
162
169
|
closed_array = []
|
163
|
-
self.title
|
170
|
+
if not self.title:
|
171
|
+
self.title = os.path.basename(irap_file).split(".")[0]
|
164
172
|
for i, poly in enumerate(inpoints):
|
165
173
|
if len(poly) > 1: # Polylines must have at least 2 points
|
166
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|
self.count_perpol.append(len(poly))
|
@@ -183,7 +191,8 @@ class PolylineSet(rql_c._BasePolyline):
|
|
183
191
|
inpoints = f.readlines()
|
184
192
|
self.count_perpol = []
|
185
193
|
closed_array = []
|
186
|
-
self.title
|
194
|
+
if not self.title:
|
195
|
+
self.title = os.path.basename(charisma_file).split(".")[0]
|
187
196
|
for i, line in enumerate(inpoints):
|
188
197
|
line = line.split()
|
189
198
|
coord_entry = np.array([[float(line[3]), float(line[4]), float(line[5])]])
|
@@ -278,32 +287,45 @@ class PolylineSet(rql_c._BasePolyline):
|
|
278
287
|
pindex.text = '0'
|
279
288
|
|
280
289
|
if self.boolnotconstant:
|
290
|
+
|
281
291
|
# We have mixed data - use a BooleanArrayFromIndexArray
|
282
292
|
closed = rqet.SubElement(patch, ns['resqml2'] + 'ClosedPolylines')
|
283
293
|
closed.set(ns['xsi'] + 'type', ns['xsd'] + 'BooleanArrayFromIndexArray')
|
284
294
|
closed.text = '\n'
|
285
295
|
|
286
|
-
bool_val = rqet.SubElement(closed, ns['resqml2'] + '
|
296
|
+
bool_val = rqet.SubElement(closed, ns['resqml2'] + 'IndexIsTrue')
|
287
297
|
bool_val.set(ns['xsi'] + 'type', ns['xsd'] + 'boolean')
|
288
|
-
bool_val.text = str(self.boolvalue).lower()
|
289
|
-
|
290
|
-
ind_val = rqet.SubElement(closed, ns['resqml2'] + 'Indices')
|
291
|
-
ind_val.set(ns['xsi'] + 'type', ns['eml'] + 'Hdf5Dataset')
|
292
|
-
ind_val.text = '\n'
|
298
|
+
bool_val.text = str(not self.boolvalue).lower()
|
293
299
|
|
294
300
|
count = rqet.SubElement(closed, ns['resqml2'] + 'Count')
|
295
301
|
count.set(ns['xsi'] + 'type', ns['xsd'] + 'positiveInteger')
|
296
302
|
count.text = str(len(self.count_perpol))
|
297
303
|
|
298
|
-
|
304
|
+
ind_val = rqet.SubElement(closed, ns['resqml2'] + 'Indices')
|
305
|
+
ind_val.set(ns['xsi'] + 'type', ns['resqml2'] + 'IntegerHdf5Array')
|
306
|
+
ind_val.text = '\n'
|
307
|
+
|
308
|
+
iv_null = rqet.SubElement(ind_val, ns['resqml2'] + 'NullValue')
|
309
|
+
iv_null.set(ns['xsi'] + 'type', ns['xsd'] + 'integer')
|
310
|
+
iv_null.text = '-1'
|
311
|
+
|
312
|
+
iv_values = rqet.SubElement(ind_val, ns['resqml2'] + 'Values')
|
313
|
+
iv_values.set(ns['xsi'] + 'type', ns['eml'] + 'Hdf5Dataset')
|
314
|
+
iv_values.text = '\n'
|
315
|
+
|
316
|
+
self.model.create_hdf5_dataset_ref(ext_uuid, self.uuid, 'indices_patch0', root = iv_values)
|
317
|
+
|
299
318
|
else:
|
319
|
+
|
300
320
|
# All bools are the same - use a BooleanConstantArray
|
301
321
|
closed = rqet.SubElement(patch, ns['resqml2'] + 'ClosedPolylines')
|
302
322
|
closed.set(ns['xsi'] + 'type', ns['resqml2'] + 'BooleanConstantArray')
|
303
323
|
closed.text = '\n'
|
324
|
+
|
304
325
|
bool_val = rqet.SubElement(closed, ns['resqml2'] + 'Value')
|
305
326
|
bool_val.set(ns['xsi'] + 'type', ns['xsd'] + 'boolean')
|
306
327
|
bool_val.text = str(self.boolvalue).lower()
|
328
|
+
|
307
329
|
count = rqet.SubElement(closed, ns['resqml2'] + 'Count')
|
308
330
|
count.set(ns['xsi'] + 'type', ns['xsd'] + 'positiveInteger')
|
309
331
|
count.text = str(len(self.count_perpol))
|
@@ -367,7 +389,7 @@ class PolylineSet(rql_c._BasePolyline):
|
|
367
389
|
if self.uuid is None:
|
368
390
|
self.uuid = bu.new_uuid()
|
369
391
|
self.combine_polylines(self.polys)
|
370
|
-
self.bool_array_format(
|
392
|
+
self.bool_array_format()
|
371
393
|
self.save_polys = save_polylines
|
372
394
|
if self.save_polys:
|
373
395
|
for poly in self.polys:
|
@@ -377,29 +399,37 @@ class PolylineSet(rql_c._BasePolyline):
|
|
377
399
|
h5_reg.register_dataset(self.uuid, 'points_patch0', self.coordinates)
|
378
400
|
h5_reg.register_dataset(self.uuid, 'NodeCountPerPolyline_patch0', self.count_perpol.astype(np.int32))
|
379
401
|
if self.boolnotconstant:
|
380
|
-
h5_reg.register_dataset(self.uuid, 'indices_patch0', self.indices)
|
402
|
+
h5_reg.register_dataset(self.uuid, 'indices_patch0', np.array(self.indices, dtype = np.int32))
|
381
403
|
h5_reg.write(file_name, mode = mode)
|
382
404
|
|
383
405
|
def get_bool_array(self, closed_node):
|
384
|
-
# TODO:
|
385
|
-
"""Returns a boolean array using details in the node location.
|
406
|
+
# TODO: check for other permissible forms of the abstract boolean array
|
407
|
+
"""Returns a boolean array using details in the xml node location.
|
386
408
|
|
387
|
-
|
409
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+
arguments:
|
410
|
+
closed_node (xml node): the node under which the boolean array information sits
|
388
411
|
|
389
|
-
|
390
|
-
|
412
|
+
returns:
|
413
|
+
1D numpy bool array set True for those pplylines within the set which are marked as closed
|
391
414
|
"""
|
392
|
-
if
|
415
|
+
# if type of boolean array is BooleanConstantArray, uses the array value and count to generate
|
416
|
+
# the array; if type of boolean array is BooleanArrayFromIndexArray, finds the "other" value
|
417
|
+
# bool and indices of the "other" values, and inserts these into an array opposite to the main bool
|
418
|
+
flavour = rqet.node_type(closed_node)
|
419
|
+
if flavour == 'BooleanConstantArray':
|
393
420
|
count = rqet.find_tag_int(closed_node, 'Count')
|
394
421
|
value = rqet.bool_from_text(rqet.node_text(rqet.find_tag(closed_node, 'Value')))
|
395
|
-
return np.full((count), value)
|
396
|
-
elif
|
422
|
+
return np.full((count,), value, dtype = bool)
|
423
|
+
elif flavour == 'BooleanArrayFromIndexArray':
|
397
424
|
count = rqet.find_tag_int(closed_node, 'Count')
|
398
|
-
|
425
|
+
indices_node = rqet.find_tag(closed_node, 'Indices')
|
426
|
+
assert indices_node is not None
|
427
|
+
indices_arr = rql_c.load_hdf5_array(self, indices_node, 'indices_arr', tag = 'Values', dtype = 'int')
|
399
428
|
istrue = rqet.bool_from_text(rqet.node_text(rqet.find_tag(closed_node, 'IndexIsTrue')))
|
400
|
-
out = np.full((count), not istrue)
|
429
|
+
out = np.full((count,), not istrue, dtype = bool)
|
401
430
|
out[indices_arr] = istrue
|
402
431
|
return out
|
432
|
+
raise ValueError(f'unrecognised closed array xml node type: {flavour}')
|
403
433
|
|
404
434
|
def convert_to_polylines(self,
|
405
435
|
closed_array = None,
|
@@ -496,32 +526,32 @@ class PolylineSet(rql_c._BasePolyline):
|
|
496
526
|
|
497
527
|
self.polys = polylines
|
498
528
|
|
499
|
-
def bool_array_format(self
|
500
|
-
"""Determines an appropriate output boolean array format
|
529
|
+
def bool_array_format(self):
|
530
|
+
"""Determines an appropriate output boolean array format depending on the closed_array bools.
|
501
531
|
|
502
532
|
self.boolnotconstant - set to True if all are not open or all closed
|
503
533
|
self.boolvalue - value of isclosed for all polylines, or for the majority of polylines if mixed
|
504
534
|
self.indices - array of indices where the values are not self.boolvalue, if the polylines are mixed
|
505
535
|
"""
|
506
536
|
|
537
|
+
assert self.closed_array is not None
|
507
538
|
self.indices = []
|
508
539
|
self.boolnotconstant = False
|
509
|
-
if all(closed_array):
|
540
|
+
if all(self.closed_array):
|
510
541
|
self.boolvalue = True
|
511
|
-
elif not
|
542
|
+
elif not any(self.closed_array):
|
512
543
|
self.boolvalue = False
|
513
544
|
else:
|
514
|
-
if np.count_nonzero(closed_array) > (len(closed_array)
|
545
|
+
if np.count_nonzero(self.closed_array) > (len(self.closed_array) // 2):
|
515
546
|
self.boolvalue = True
|
516
|
-
for i, val in enumerate(closed_array):
|
547
|
+
for i, val in enumerate(self.closed_array):
|
517
548
|
if not val:
|
518
549
|
self.indices.append(i)
|
519
550
|
else:
|
520
551
|
self.boolvalue = False
|
521
|
-
for i, val in enumerate(closed_array):
|
552
|
+
for i, val in enumerate(self.closed_array):
|
522
553
|
if val:
|
523
554
|
self.indices.append(i)
|
524
|
-
if len(self.indices) > 0:
|
525
555
|
self.boolnotconstant = True
|
526
556
|
|
527
557
|
def set_interpretation_root(self, rep_int_root, recursive = True):
|
resqpy/model/_hdf5.py
CHANGED
@@ -208,12 +208,15 @@ def _h5_array_element(model,
|
|
208
208
|
if object is None:
|
209
209
|
object = model
|
210
210
|
|
211
|
-
|
211
|
+
if isinstance(dtype, str) and dtype == 'pack':
|
212
|
+
dtype = bool
|
213
|
+
|
214
|
+
# check if attribute has already been cached
|
212
215
|
if array_attribute is not None:
|
213
216
|
existing_value = getattr(object, array_attribute, None)
|
214
217
|
|
215
218
|
# Watch out for np.array(None): check existing_value has a valid "shape"
|
216
|
-
if existing_value is not None and getattr(existing_value,
|
219
|
+
if existing_value is not None and getattr(existing_value, 'shape', False):
|
217
220
|
if index is None:
|
218
221
|
return None # this option allows caching of array without actually referring to any element
|
219
222
|
return existing_value[tuple(index)]
|
@@ -222,14 +225,20 @@ def _h5_array_element(model,
|
|
222
225
|
if h5_root is None:
|
223
226
|
return None
|
224
227
|
if cache_array:
|
228
|
+
str_dtype = str(dtype)
|
225
229
|
shape_tuple = tuple(h5_root[h5_key_pair[1]].shape)
|
226
|
-
if required_shape is None
|
227
|
-
|
230
|
+
if required_shape is None:
|
231
|
+
required_shape = shape_tuple
|
232
|
+
object.__dict__[array_attribute] = np.zeros(required_shape, dtype = dtype)
|
233
|
+
if shape_tuple == required_shape:
|
228
234
|
object.__dict__[array_attribute][:] = h5_root[h5_key_pair[1]]
|
235
|
+
elif (len(shape_tuple) == len(required_shape) and ('bool' in str_dtype or 'int8' in str_dtype) and
|
236
|
+
8 * (shape_tuple[-1] - 1) < required_shape[-1] <= 8 * shape_tuple[-1]):
|
237
|
+
a = np.unpackbits(h5_root[h5_key_pair[1]], axis = -1).astype(bool)
|
238
|
+
object.__dict__[array_attribute][:] = a[..., :required_shape[-1]]
|
229
239
|
else:
|
230
|
-
object.__dict__[array_attribute] =
|
231
|
-
|
232
|
-
dtype = dtype).reshape(required_shape)
|
240
|
+
object.__dict__[array_attribute][:] = \
|
241
|
+
np.array(h5_root[h5_key_pair[1]], dtype = dtype).reshape(required_shape)
|
233
242
|
_h5_release(model)
|
234
243
|
if index is None:
|
235
244
|
return None
|
@@ -241,6 +250,7 @@ def _h5_array_element(model,
|
|
241
250
|
result = h5_root[h5_key_pair[1]][tuple(index)]
|
242
251
|
else:
|
243
252
|
shape_tuple = tuple(h5_root[h5_key_pair[1]].shape)
|
253
|
+
# todo: handle unpacking of a single bit into a bool?
|
244
254
|
if shape_tuple == required_shape:
|
245
255
|
result = h5_root[h5_key_pair[1]][tuple(index)]
|
246
256
|
else:
|
resqpy/model/_model.py
CHANGED
@@ -1344,7 +1344,8 @@ class Model():
|
|
1344
1344
|
required to cache or access cached array
|
1345
1345
|
dtype (string or data type): the data type of the elements of the array (need not match hdf5 array in precision)
|
1346
1346
|
required_shape (tuple of ints, optional): if not None, the hdf5 array will be reshaped to this shape; if index
|
1347
|
-
is not None, it is taken to be applicable to the required shape
|
1347
|
+
is not None, it is taken to be applicable to the required shape; required if the array is bool data that was
|
1348
|
+
written with resqpy specific dtype of 'pack'
|
1348
1349
|
|
1349
1350
|
returns:
|
1350
1351
|
if index is None, then None;
|
resqpy/model/_xml.py
CHANGED
@@ -153,9 +153,9 @@ def _create_ref_node(model, flavour, title, uuid, content_type = None, root = No
|
|
153
153
|
else:
|
154
154
|
ct_node.text = 'application/x-resqml+xml;version=2.0;type=' + content_type
|
155
155
|
|
156
|
-
if
|
156
|
+
if title is None or len(title) == 0:
|
157
157
|
title = model.title(uuid = uuid)
|
158
|
-
if title is None:
|
158
|
+
if title is None or len(title) == 0:
|
159
159
|
title = 'untitled'
|
160
160
|
title_node = rqet.SubElement(ref_node, ns['eml'] + 'Title')
|
161
161
|
title_node.set(ns['xsi'] + 'type', ns['eml'] + 'DescriptionString')
|
@@ -204,8 +204,8 @@ def _create_rels_part(model):
|
|
204
204
|
def _create_citation(root = None, title = '', originator = None):
|
205
205
|
"""Creates a citation xml node and optionally appends as a child of root."""
|
206
206
|
|
207
|
-
if title is None:
|
208
|
-
title = ''
|
207
|
+
if title is None or len(title) == 0:
|
208
|
+
title = 'untitled'
|
209
209
|
|
210
210
|
citation = rqet.Element(ns['eml'] + 'Citation')
|
211
211
|
citation.set(ns['xsi'] + 'type', ns['eml'] + 'Citation')
|
@@ -80,6 +80,7 @@ def function_multiprocessing(function: Callable,
|
|
80
80
|
if tmp_dir_path is None:
|
81
81
|
tmp_dir_path = '.'
|
82
82
|
tmp_dir = Path(tmp_dir_path) / f'tmp_{uuid.uuid4()}'
|
83
|
+
os.makedirs(tmp_dir)
|
83
84
|
for i, kwargs in enumerate(kwargs_list):
|
84
85
|
kwargs["index"] = i
|
85
86
|
kwargs["parent_tmp_dir"] = str(tmp_dir)
|
@@ -33,12 +33,15 @@ def find_faces_to_represent_surface_regular_wrapper(
|
|
33
33
|
trimmed: bool = False,
|
34
34
|
is_curtain = False,
|
35
35
|
extend_fault_representation: bool = False,
|
36
|
+
flange_inner_ring = False,
|
37
|
+
saucer_parameter = None,
|
36
38
|
retriangulate: bool = False,
|
37
39
|
related_uuid = None,
|
38
40
|
progress_fn: Optional[Callable] = None,
|
39
41
|
extra_metadata = None,
|
40
42
|
return_properties: Optional[List[str]] = None,
|
41
|
-
raw_bisector: bool = False
|
43
|
+
raw_bisector: bool = False,
|
44
|
+
use_pack: bool = False) -> Tuple[int, bool, str, List[Union[UUID, str]]]:
|
42
45
|
"""Multiprocessing wrapper function of find_faces_to_represent_surface_regular_optimised.
|
43
46
|
|
44
47
|
arguments:
|
@@ -79,6 +82,8 @@ def find_faces_to_represent_surface_regular_wrapper(
|
|
79
82
|
the returned dictionary has the passed strings as keys and numpy arrays as values
|
80
83
|
raw_bisector (bool, default False): if True and grid bisector is requested then it is left in a raw
|
81
84
|
form without assessing which side is shallower (True values indicate same side as origin cell)
|
85
|
+
use_pack (bool, default False): if True, boolean properties will be stored in numpy packed format,
|
86
|
+
which will only be readable by resqpy based applications
|
82
87
|
|
83
88
|
returns:
|
84
89
|
Tuple containing:
|
@@ -150,6 +155,8 @@ def find_faces_to_represent_surface_regular_wrapper(
|
|
150
155
|
convexity_parameter = 2.0,
|
151
156
|
reorient = True,
|
152
157
|
extend_with_flange = extend_fault_representation,
|
158
|
+
flange_inner_ring = flange_inner_ring,
|
159
|
+
saucer_parameter = saucer_parameter,
|
153
160
|
flange_radial_distance = flange_radius,
|
154
161
|
make_clockwise = False)
|
155
162
|
extended = extend_fault_representation
|
@@ -181,6 +188,8 @@ def find_faces_to_represent_surface_regular_wrapper(
|
|
181
188
|
convexity_parameter = 2.0,
|
182
189
|
reorient = True,
|
183
190
|
extend_with_flange = extend_fault_representation,
|
191
|
+
flange_inner_ring = flange_inner_ring,
|
192
|
+
saucer_parameter = saucer_parameter,
|
184
193
|
flange_radial_distance = flange_radius,
|
185
194
|
make_clockwise = False)
|
186
195
|
del pset
|
@@ -345,13 +354,13 @@ def find_faces_to_represent_surface_regular_wrapper(
|
|
345
354
|
raise ValueError(f'unrecognised property name {p_name}')
|
346
355
|
if property_collection.number_of_imports() > 0:
|
347
356
|
# log.debug('writing gcs property hdf5 data')
|
348
|
-
property_collection.write_hdf5_for_imported_list()
|
357
|
+
property_collection.write_hdf5_for_imported_list(use_pack = use_pack)
|
349
358
|
uuids_properties = property_collection.create_xml_for_imported_list_and_add_parts_to_model(
|
350
359
|
find_local_property_kinds = True)
|
351
360
|
uuid_list.extend(uuids_properties)
|
352
361
|
if grid_pc is not None and grid_pc.number_of_imports() > 0:
|
353
362
|
# log.debug('writing grid property (bisector) hdf5 data')
|
354
|
-
grid_pc.write_hdf5_for_imported_list()
|
363
|
+
grid_pc.write_hdf5_for_imported_list(use_pack = use_pack)
|
355
364
|
# log.debug('creating xml for grid property (bisector)')
|
356
365
|
uuids_properties = grid_pc.create_xml_for_imported_list_and_add_parts_to_model(
|
357
366
|
find_local_property_kinds = True)
|
resqpy/olio/intersection.py
CHANGED
@@ -76,7 +76,7 @@ def line_triangle_intersect(line_p, line_v, triangle, line_segment = False, l_to
|
|
76
76
|
return line_p + t * line_v
|
77
77
|
|
78
78
|
|
79
|
-
@njit
|
79
|
+
@njit # pragma: no cover
|
80
80
|
def line_triangle_intersect_numba(
|
81
81
|
line_p: np.ndarray,
|
82
82
|
line_v: np.ndarray,
|
@@ -164,8 +164,7 @@ def line_triangles_intersects(line_p, line_v, triangles, line_segment = False):
|
|
164
164
|
ts[:] = np.where(np.logical_or(ts < 0.0, ts > 1.0), np.nan, ts)
|
165
165
|
np.divide(np.sum(np.cross(p02s, line_rv) * lp_t0s, axis = 1), denoms, out = us, where = nz)
|
166
166
|
np.divide(np.sum(np.cross(line_rv, p01s) * lp_t0s, axis = 1), denoms, out = vs, where = nz)
|
167
|
-
ts[
|
168
|
-
ts)
|
167
|
+
ts[np.where(np.logical_or(np.logical_or(us < 0.0, us > 1.0), np.logical_or(vs < 0.0, us + vs > 1.0)))] = np.nan
|
169
168
|
|
170
169
|
intersects = np.empty((n, 3))
|
171
170
|
intersects[:] = line_v * np.repeat(ts, 3).reshape((n, 3)) + line_p
|
resqpy/olio/read_nexus_fault.py
CHANGED
@@ -13,8 +13,8 @@ import numpy as np
|
|
13
13
|
import pandas as pd
|
14
14
|
|
15
15
|
|
16
|
-
def
|
17
|
-
"""Reads a Nexus (!) format file containing one or more MULT keywords and returns a dataframe with the MULT rows."""
|
16
|
+
def load_nexus_fault_mult_table_from_list(file_as_list):
|
17
|
+
"""Reads a Nexus (!) format list of file contents containing one or more MULT keywords and returns a dataframe with the MULT rows."""
|
18
18
|
|
19
19
|
def is_number(s):
|
20
20
|
try:
|
@@ -41,70 +41,18 @@ def load_nexus_fault_mult_table(file_name):
|
|
41
41
|
|
42
42
|
face_dict = {'TX': 'I', 'TY': 'J', 'TZ': 'K', 'TI': 'I', 'TJ': 'J', 'TK': 'K'}
|
43
43
|
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
# line = line.partition('C')[0] # removing trailing comments
|
52
|
-
tokens = line.split()
|
53
|
-
if ISTABLE:
|
54
|
-
if is_number(tokens[0]):
|
55
|
-
ISRECORD = True
|
56
|
-
|
57
|
-
if ISRECORD and (not is_number(tokens[0])):
|
58
|
-
data = chunks[0:]
|
59
|
-
d_elems = np.array([np.array(data[i].split()) for i in range(len(data))])
|
60
|
-
# fill empty elements with zero
|
61
|
-
lens = np.array([len(i) for i in d_elems])
|
62
|
-
# Mask of valid places in each row
|
63
|
-
mask = np.arange(lens.max()) < lens[:, None]
|
64
|
-
# Setup output array and put elements from data into masked positions
|
65
|
-
outdata = np.zeros(mask.shape, dtype = d_elems.dtype)
|
66
|
-
outdata[mask] = np.concatenate(d_elems)
|
67
|
-
df = pd.DataFrame(outdata)
|
68
|
-
for column in df.columns:
|
69
|
-
df[column] = pd.to_numeric(df[column], errors = 'ignore')
|
70
|
-
df.columns = ['i1', 'i2', 'j1', 'j2', 'k1', 'k2', 'mult']
|
71
|
-
df['grid'] = grid
|
72
|
-
df['name'] = name
|
73
|
-
df['face'] = face
|
74
|
-
dfs.append(df)
|
75
|
-
num_tables += 1
|
76
|
-
|
77
|
-
ISTABLE = False
|
78
|
-
ISRECORD = False
|
79
|
-
chunks = []
|
80
|
-
|
81
|
-
if ISTABLE:
|
82
|
-
if re.match("(.*)GRID(.*)", tokens[0]):
|
83
|
-
if len(tokens) > 0:
|
84
|
-
grid = tokens[1]
|
85
|
-
elif re.match("(.*)FNAME(.*)", tokens[0]):
|
86
|
-
if len(tokens) > 0:
|
87
|
-
name = tokens[1]
|
88
|
-
else:
|
89
|
-
if re.match(r"^MULT$", tokens[0]):
|
90
|
-
ISTABLE = False
|
91
|
-
ISRECORD = False
|
92
|
-
chunks = []
|
93
|
-
else:
|
94
|
-
chunks.append(line.strip())
|
95
|
-
|
96
|
-
if re.match(r"^MULT$", tokens[0]):
|
97
|
-
if len(tokens) > 0:
|
98
|
-
face = face_dict[tokens[1]]
|
99
|
-
if 'MINUS' in tokens:
|
100
|
-
face += '-' # indicates data apply to 'negative' faces of specified cells
|
101
|
-
grid = 'ROOT' # nexus default
|
102
|
-
name = 'NONE'
|
103
|
-
ISTABLE = True
|
104
|
-
|
105
|
-
else:
|
44
|
+
chunks = []
|
45
|
+
for line in file_as_list:
|
46
|
+
if len(line.strip()):
|
47
|
+
if (not line.strip()[0] == '!') & (not line.strip()[0] == 'C'):
|
48
|
+
line = line.partition('!')[0] # removing trailing comments
|
49
|
+
# line = line.partition('C')[0] # removing trailing comments
|
50
|
+
tokens = line.split()
|
106
51
|
if ISTABLE:
|
107
|
-
if
|
52
|
+
if is_number(tokens[0]):
|
53
|
+
ISRECORD = True
|
54
|
+
|
55
|
+
if ISRECORD and (not is_number(tokens[0])):
|
108
56
|
data = chunks[0:]
|
109
57
|
d_elems = np.array([np.array(data[i].split()) for i in range(len(data))])
|
110
58
|
# fill empty elements with zero
|
@@ -128,6 +76,59 @@ def load_nexus_fault_mult_table(file_name):
|
|
128
76
|
ISRECORD = False
|
129
77
|
chunks = []
|
130
78
|
|
79
|
+
if ISTABLE:
|
80
|
+
if re.match("(.*)GRID(.*)", tokens[0]):
|
81
|
+
if len(tokens) > 0:
|
82
|
+
grid = tokens[1]
|
83
|
+
elif re.match("(.*)FNAME(.*)", tokens[0]):
|
84
|
+
if len(tokens) > 0:
|
85
|
+
name = tokens[1]
|
86
|
+
else:
|
87
|
+
if re.match(r"^MULT$", tokens[0]):
|
88
|
+
ISTABLE = False
|
89
|
+
ISRECORD = False
|
90
|
+
chunks = []
|
91
|
+
else:
|
92
|
+
chunks.append(line.strip())
|
93
|
+
|
94
|
+
if re.match(r"^MULT$", tokens[0]):
|
95
|
+
if len(tokens) > 0:
|
96
|
+
face = face_dict[tokens[1]]
|
97
|
+
if 'MINUS' in tokens:
|
98
|
+
face += '-' # indicates data apply to 'negative' faces of specified cells
|
99
|
+
grid = 'ROOT' # nexus default
|
100
|
+
name = 'NONE'
|
101
|
+
ISTABLE = True
|
102
|
+
|
103
|
+
else:
|
104
|
+
if ISTABLE:
|
105
|
+
if ISRECORD:
|
106
|
+
data = chunks[0:]
|
107
|
+
d_elems = np.array([np.array(data[i].split()) for i in range(len(data))])
|
108
|
+
# fill empty elements with zero
|
109
|
+
lens = np.array([len(i) for i in d_elems])
|
110
|
+
# Mask of valid places in each row
|
111
|
+
mask = np.arange(lens.max()) < lens[:, None]
|
112
|
+
# Setup output array and put elements from data into masked positions
|
113
|
+
outdata = np.zeros(mask.shape, dtype = d_elems.dtype)
|
114
|
+
outdata[mask] = np.concatenate(d_elems)
|
115
|
+
df = pd.DataFrame(outdata)
|
116
|
+
for column in df.columns:
|
117
|
+
df[column] = pd.to_numeric(df[column], errors = 'ignore')
|
118
|
+
df.columns = ['i1', 'i2', 'j1', 'j2', 'k1', 'k2', 'mult']
|
119
|
+
df['grid'] = grid
|
120
|
+
df['name'] = name
|
121
|
+
df['face'] = face
|
122
|
+
dfs.append(df)
|
123
|
+
num_tables += 1
|
124
|
+
|
125
|
+
ISTABLE = False
|
126
|
+
ISRECORD = False
|
127
|
+
chunks = []
|
128
|
+
|
129
|
+
if not dfs:
|
130
|
+
return pd.DataFrame()
|
131
|
+
|
131
132
|
fault_df = pd.concat(dfs).reset_index(drop = True)
|
132
133
|
|
133
134
|
convert_dict = {'i1': int, 'i2': int, 'j1': int, 'j2': int, 'k1': int, 'k2': int, 'mult': float}
|
@@ -136,7 +137,10 @@ def load_nexus_fault_mult_table(file_name):
|
|
136
137
|
return fault_df
|
137
138
|
|
138
139
|
|
139
|
-
def
|
140
|
+
def load_nexus_fault_mult_table(file_name):
|
140
141
|
"""Reads a Nexus (!) format file containing one or more MULT keywords and returns a dataframe with the MULT rows."""
|
141
142
|
|
142
|
-
|
143
|
+
with open(file_name) as f:
|
144
|
+
file_as_list = f.readlines()
|
145
|
+
|
146
|
+
return load_nexus_fault_mult_table_from_list(file_as_list)
|