brukerapi 0.2.3__tar.gz → 0.2.5__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (39) hide show
  1. {brukerapi-0.2.3/brukerapi.egg-info → brukerapi-0.2.5}/PKG-INFO +1 -1
  2. brukerapi-0.2.5/brukerapi/config/properties_traj_core.json +188 -0
  3. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/dataset.py +6 -5
  4. {brukerapi-0.2.3 → brukerapi-0.2.5/brukerapi.egg-info}/PKG-INFO +1 -1
  5. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/SOURCES.txt +2 -1
  6. {brukerapi-0.2.3 → brukerapi-0.2.5}/pyproject.toml +1 -1
  7. brukerapi-0.2.5/test/test_trajectory.py +27 -0
  8. brukerapi-0.2.3/brukerapi/config/properties_traj_core.json +0 -109
  9. {brukerapi-0.2.3 → brukerapi-0.2.5}/LICENSE +0 -0
  10. {brukerapi-0.2.3 → brukerapi-0.2.5}/MANIFEST.in +0 -0
  11. {brukerapi-0.2.3 → brukerapi-0.2.5}/README.rst +0 -0
  12. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/__init__.py +0 -0
  13. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/cli.py +0 -0
  14. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_2dseq_core.json +0 -0
  15. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_2dseq_custom.json +0 -0
  16. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_fid_core.json +0 -0
  17. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_fid_custom.json +0 -0
  18. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_rawdata_core.json +0 -0
  19. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_rawdata_custom.json +0 -0
  20. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/config/properties_traj_custom.json +0 -0
  21. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/data.py +0 -0
  22. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/exceptions.py +0 -0
  23. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/folders.py +0 -0
  24. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/jcampdx.py +0 -0
  25. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/mergers.py +0 -0
  26. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/schemas.py +0 -0
  27. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/splitters.py +0 -0
  28. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/utils.py +0 -0
  29. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/dependency_links.txt +0 -0
  30. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/entry_points.txt +0 -0
  31. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/not-zip-safe +0 -0
  32. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/requires.txt +0 -0
  33. {brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/top_level.txt +0 -0
  34. {brukerapi-0.2.3 → brukerapi-0.2.5}/setup.cfg +0 -0
  35. {brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_dataset.py +0 -0
  36. {brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_exceptions.py +0 -0
  37. {brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_jcampdx.py +0 -0
  38. {brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_random_access.py +0 -0
  39. {brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_split.py +0 -0
{brukerapi-0.2.3/brukerapi.egg-info → brukerapi-0.2.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: brukerapi
3
- Version: 0.2.3
3
+ Version: 0.2.5
4
4
  Summary: Bruker API
5
5
  Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
6
6
  Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
brukerapi-0.2.5/brukerapi/config/properties_traj_core.json ADDED
@@ -0,0 +1,188 @@
1
+ {
2
+ "numpy_dtype": [
3
+ {
4
+ "cmd": "np.dtype('f8')",
5
+ "conditions": []
6
+ }
7
+ ],
8
+ "scheme_id": [
9
+ {
10
+ "cmd": "'RADIAL'",
11
+ "conditions": [
12
+ [
13
+ "#PULPROG[1:-1]",
14
+ [
15
+ "UTE.ppg",
16
+ "UTE3D.ppg",
17
+ "IgUTE.ppg",
18
+ "ZTE.ppg"
19
+ ]
20
+ ],
21
+ [
22
+ "#ACQ_sw_version",
23
+ [
24
+ "<PV 6.0.1>",
25
+ "<PV 5.1>",
26
+ "<PV-7.0.0>",
27
+ "<PV-360.3.0>",
28
+ "<PV-360.3.1>",
29
+ "<PV-360.3.2>",
30
+ "<PV-360.3.3>",
31
+ "<PV-360.3.4>",
32
+ "<PV-360.3.5>",
33
+ "<PV-360.3.6>",
34
+ "<PV-360.3.7>"
35
+ ]
36
+ ]
37
+ ]
38
+ },
39
+ {
40
+ "cmd": "'SPIRAL'",
41
+ "conditions": [
42
+ [
43
+ "#PULPROG[1:-1]",
44
+ [
45
+ "SPIRAL.ppg",
46
+ "DtiSpiral.ppg"
47
+ ]
48
+ ],
49
+ [
50
+ "#ACQ_sw_version",
51
+ [
52
+ "<PV 6.0.1>",
53
+ "<PV 5.1>",
54
+ "<PV-7.0.0>",
55
+ "<PV-360.3.0>",
56
+ "<PV-360.3.1>",
57
+ "<PV-360.3.2>",
58
+ "<PV-360.3.3>",
59
+ "<PV-360.3.4>",
60
+ "<PV-360.3.5>",
61
+ "<PV-360.3.6>",
62
+ "<PV-360.3.7>"
63
+ ]
64
+ ]
65
+ ]
66
+ },
67
+ {
68
+ "cmd": "'ZTE'",
69
+ "conditions": [
70
+ [
71
+ "#PULPROG[1:-1]",
72
+ [
73
+ "ZTE.ppg"
74
+ ]
75
+ ],
76
+ [
77
+ "#ACQ_sw_version",
78
+ [
79
+ "<PV 6.0.1>",
80
+ "<PV 5.1>"
81
+ ]
82
+ ]
83
+ ]
84
+ }
85
+ ],
86
+ "traj_type": [
87
+ {
88
+ "cmd": "'radial'",
89
+ "conditions": [
90
+ [
91
+ "@scheme_id",
92
+ [
93
+ "RADIAL",
94
+ "ZTE"
95
+ ]
96
+ ]
97
+ ]
98
+ },
99
+ {
100
+ "cmd": "'spiral'",
101
+ "conditions": [
102
+ [
103
+ "@scheme_id",
104
+ [
105
+ "SPIRAL"
106
+ ]
107
+ ]
108
+ ]
109
+ }
110
+ ],
111
+ "shape_storage": [
112
+ {
113
+ "cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro), #NPro)",
114
+ "conditions": [
115
+ [
116
+ "@scheme_id",
117
+ [
118
+ "RADIAL",
119
+ "ZTE"
120
+ ]
121
+ ]
122
+ ]
123
+ },
124
+ {
125
+ "cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves), #PVM_SpiralNbOfInterleaves)",
126
+ "conditions": [
127
+ [
128
+ "@scheme_id",
129
+ [
130
+ "SPIRAL"
131
+ ]
132
+ ]
133
+ ]
134
+ }
135
+ ],
136
+ "permute": [
137
+ {
138
+ "cmd": [
139
+ 0,
140
+ 1,
141
+ 2
142
+ ],
143
+ "conditions": [
144
+ [
145
+ "@scheme_id",
146
+ [
147
+ "RADIAL",
148
+ "ZTE",
149
+ "SPIRAL"
150
+ ]
151
+ ]
152
+ ]
153
+ }
154
+ ],
155
+ "final": [
156
+ {
157
+ "cmd": [
158
+ "#ACQ_dim",
159
+ "int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro)",
160
+ "#NPro"
161
+ ],
162
+ "conditions": [
163
+ [
164
+ "@scheme_id",
165
+ [
166
+ "RADIAL",
167
+ "ZTE"
168
+ ]
169
+ ]
170
+ ]
171
+ },
172
+ {
173
+ "cmd": [
174
+ "#ACQ_dim",
175
+ "int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves)",
176
+ "#PVM_SpiralNbOfInterleaves"
177
+ ],
178
+ "conditions": [
179
+ [
180
+ "@scheme_id",
181
+ [
182
+ "SPIRAL"
183
+ ]
184
+ ]
185
+ ]
186
+ }
187
+ ]
188
+ }
{brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/dataset.py RENAMED
@@ -291,7 +291,7 @@ class Dataset:
291
291
 
292
292
  self.load_schema()
293
293
  self.load_data()
294
- # self.load_traj()
294
+ self.load_traj()
295
295
 
296
296
  def unload(self):
297
297
  """
@@ -455,7 +455,7 @@ class Dataset:
455
455
  :return: value of property, or list of values of properties
456
456
  """
457
457
  if isinstance(cmd, str):
458
- return eval(self._sub_parameters(cmd))
458
+ return eval(self._sub_parameters(cmd), {**globals(), "self": self})
459
459
  if isinstance(cmd, (int, float)):
460
460
  return cmd
461
461
  if isinstance(cmd, list):
@@ -588,9 +588,10 @@ class Dataset:
588
588
 
589
589
  def load_traj(self, **kwargs):
590
590
  if Path(self.path.parent / "traj").exists() and self.type != "traj":
591
- self._traj = Dataset(self.path.parent / "traj", load=False, random_access=self.random_access)
591
+ self._traj = Dataset(self.path.parent / "traj", load=LOAD_STAGES["empty"])
592
592
  self._traj._parameters = self.parameters
593
- self._traj._schema = SchemaTraj(self._traj, meta=self.schema._meta, sub_params=self.schema._sub_params, fid=self)
593
+ self._traj.load_properties()
594
+ self._traj._schema = SchemaTraj(self._traj)
594
595
  self._traj.load_data()
595
596
  else:
596
597
  self._traj = None
@@ -730,7 +731,7 @@ class Dataset:
730
731
 
731
732
  for q in query:
732
733
  try:
733
- if not eval(self._sub_parameters(q)):
734
+ if not eval(self._sub_parameters(q), {**globals(), "self": self}):
734
735
  raise FilterEvalFalse
735
736
  except (KeyError, AttributeError) as e:
736
737
  raise FilterEvalFalse from e
{brukerapi-0.2.3 → brukerapi-0.2.5/brukerapi.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: brukerapi
3
- Version: 0.2.3
3
+ Version: 0.2.5
4
4
  Summary: Bruker API
5
5
  Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
6
6
  Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
{brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi.egg-info/SOURCES.txt RENAMED
@@ -33,4 +33,5 @@ test/test_dataset.py
33
33
  test/test_exceptions.py
34
34
  test/test_jcampdx.py
35
35
  test/test_random_access.py
36
- test/test_split.py
36
+ test/test_split.py
37
+ test/test_trajectory.py
{brukerapi-0.2.3 → brukerapi-0.2.5}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "brukerapi"
7
- version = "0.2.3"
7
+ version = "0.2.5"
8
8
  description = "Bruker API"
9
9
  authors = [
10
10
  { name = "Tomas Psorn", email = "tomaspsorn@isibrno.cz" },
brukerapi-0.2.5/test/test_trajectory.py ADDED
@@ -0,0 +1,27 @@
1
+ from pathlib import Path
2
+
3
+ import pytest
4
+
5
+ from brukerapi.dataset import Dataset
6
+
7
+ TRAJ_PATHS = sorted(Path("test/test_data").rglob("traj"))
8
+
9
+
10
+ @pytest.mark.parametrize("traj_path", TRAJ_PATHS, ids=[str(path) for path in TRAJ_PATHS])
11
+ def test_traj_loads_directly(traj_path):
12
+ dataset = Dataset(traj_path)
13
+
14
+ assert dataset.data.shape == dataset.shape_storage
15
+ assert dataset.data.size > 0
16
+
17
+
18
+ @pytest.mark.parametrize("traj_path", TRAJ_PATHS, ids=[str(path) for path in TRAJ_PATHS])
19
+ def test_traj_loads_from_parent_fid(traj_path):
20
+ parent_path = traj_path.parent / "fid"
21
+ if not parent_path.exists():
22
+ parent_path = traj_path.parent / "rawdata.job0"
23
+
24
+ dataset = Dataset(parent_path)
25
+
26
+ assert dataset.traj.shape == dataset._traj.shape_storage
27
+ assert dataset.traj.size > 0
brukerapi-0.2.3/brukerapi/config/properties_traj_core.json DELETED
@@ -1,109 +0,0 @@
1
- {
2
- "numpy_dtype": [
3
- {
4
- "cmd": "np.dtype('i4')",
5
- "conditions": []
6
- }
7
- ],
8
- "scheme_id": [
9
- {
10
- "cmd": "'RADIAL'" ,
11
- "conditions": [
12
- ["#PULPROG[1:-1]",
13
- [
14
- "UTE.ppg",
15
- "UTE3D.ppg",
16
- "ZTE.ppg"
17
- ]
18
- ],
19
- ["#ACQ_sw_version",
20
- [
21
- "<PV 6.0.1>",
22
- "<PV 5.1>"
23
- ]
24
- ]
25
- ]
26
- },
27
- {
28
- "cmd": "'SPIRAL'" ,
29
- "conditions": [
30
- ["#PULPROG[1:-1]",
31
- [
32
- "SPIRAL.ppg",
33
- "DtiSpiral.ppg"
34
- ]
35
- ],
36
- ["#ACQ_sw_version",
37
- [
38
- "<PV 6.0.1>",
39
- "<PV 5.1>"
40
- ]
41
- ]
42
- ]
43
- },
44
- {
45
- "cmd": "'ZTE'" ,
46
- "conditions": [
47
- ["#PULPROG[1:-1]",
48
- [
49
- "ZTE.ppg"
50
- ]
51
- ],
52
- ["#ACQ_sw_version",
53
- [
54
- "<PV 6.0.1>",
55
- "<PV 5.1>"
56
- ]
57
- ]
58
- ]
59
- }
60
- ],
61
- "traj_type": [
62
- {
63
- "cmd": "'radial'",
64
- "conditions": [["@scheme_id",["'RADIAL'","'ZTE'"]]]
65
- },
66
- {
67
- "cmd": "'spiral'",
68
- "conditions": [["@scheme_id",["SPIRAL"]]]
69
- }
70
- ],
71
- "shape_storage": [
72
- {
73
- "cmd": "(#ACQ_dim,#ACQ_size[0]//2,#NPro)",
74
- "conditions": [["@scheme_id",["RADIAL","ZTE"]]]
75
- },
76
- {
77
- "cmd": "(#ACQ_dim,#ACQ_size[0]//2,#PVM_SpiralNbOfInterleaves)",
78
- "conditions": [["@scheme_id",["SPIRAL"]]]
79
- }
80
- ],
81
- "permute": [
82
- {
83
- "cmd": [
84
- 0,
85
- 1,
86
- 2
87
- ],
88
- "conditions": [["@scheme_id",["RADIAL","ZTE","SPIRAL"]]]
89
- }
90
- ],
91
- "final": [
92
- {
93
- "cmd": [
94
- "#ACQ_dim",
95
- "#ACQ_size[0]//2",
96
- "#NPro"
97
- ],
98
- "conditions": [["@scheme_id",["RADIAL","ZTE"]]]
99
- },
100
- {
101
- "cmd": [
102
- "#ACQ_dim",
103
- "#ACQ_size[0]//2",
104
- "#PVM_SpiralNbOfInterleaves"
105
- ],
106
- "conditions": [["@scheme_id",["SPIRAL"]]]
107
- }
108
- ]
109
- }
{brukerapi-0.2.3 → brukerapi-0.2.5}/LICENSE RENAMED
File without changes
{brukerapi-0.2.3 → brukerapi-0.2.5}/MANIFEST.in RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.5}/README.rst RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/cli.py RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/data.py RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.5}/brukerapi/utils.py RENAMED
File without changes
{brukerapi-0.2.3 → brukerapi-0.2.5}/setup.cfg RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.5}/test/test_split.py RENAMED
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