brukerapi 0.2.3__tar.gz → 0.2.4__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-0.2.4}/PKG-INFO +1 -1
  2. brukerapi-0.2.4/brukerapi/config/properties_traj_core.json +188 -0
  3. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/dataset.py +4 -3
  4. {brukerapi-0.2.3 → brukerapi-0.2.4/brukerapi.egg-info}/PKG-INFO +1 -1
  5. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/SOURCES.txt +2 -1
  6. {brukerapi-0.2.3 → brukerapi-0.2.4}/pyproject.toml +1 -1
  7. brukerapi-0.2.4/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-0.2.4}/LICENSE +0 -0
  10. {brukerapi-0.2.3 → brukerapi-0.2.4}/MANIFEST.in +0 -0
  11. {brukerapi-0.2.3 → brukerapi-0.2.4}/README.rst +0 -0
  12. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/__init__.py +0 -0
  13. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/cli.py +0 -0
  14. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_2dseq_core.json +0 -0
  15. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_2dseq_custom.json +0 -0
  16. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_fid_core.json +0 -0
  17. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_fid_custom.json +0 -0
  18. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_rawdata_core.json +0 -0
  19. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_rawdata_custom.json +0 -0
  20. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/config/properties_traj_custom.json +0 -0
  21. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/data.py +0 -0
  22. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/exceptions.py +0 -0
  23. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/folders.py +0 -0
  24. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/jcampdx.py +0 -0
  25. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/mergers.py +0 -0
  26. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/schemas.py +0 -0
  27. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/splitters.py +0 -0
  28. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/utils.py +0 -0
  29. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/dependency_links.txt +0 -0
  30. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/entry_points.txt +0 -0
  31. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/not-zip-safe +0 -0
  32. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/requires.txt +0 -0
  33. {brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi.egg-info/top_level.txt +0 -0
  34. {brukerapi-0.2.3 → brukerapi-0.2.4}/setup.cfg +0 -0
  35. {brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_dataset.py +0 -0
  36. {brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_exceptions.py +0 -0
  37. {brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_jcampdx.py +0 -0
  38. {brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_random_access.py +0 -0
  39. {brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_split.py +0 -0
{brukerapi-0.2.3/brukerapi.egg-info → brukerapi-0.2.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: brukerapi
3
- Version: 0.2.3
3
+ Version: 0.2.4
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-0.2.4/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>",
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+ "<PV-360.3.3>",
31
+ "<PV-360.3.4>",
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+ "<PV-360.3.5>",
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+ "<PV-360.3.6>",
34
+ "<PV-360.3.7>"
35
+ ]
36
+ ]
37
+ ]
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+ },
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+ {
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
+ ]
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+ ]
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+ ]
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+ },
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+ {
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+ "cmd": "'spiral'",
101
+ "conditions": [
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+ [
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+ "@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
+ ]
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+ }
{brukerapi-0.2.3 → brukerapi-0.2.4}/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
  """
@@ -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
{brukerapi-0.2.3 → brukerapi-0.2.4/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: 0.2.4
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-0.2.4}/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-0.2.4}/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 = "0.2.4"
8
8
  description = "Bruker API"
9
9
  authors = [
10
10
  { name = "Tomas Psorn", email = "tomaspsorn@isibrno.cz" },
brukerapi-0.2.4/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-0.2.4}/LICENSE RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/MANIFEST.in RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/README.rst RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/cli.py RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/data.py RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/brukerapi/utils.py RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/setup.cfg RENAMED
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{brukerapi-0.2.3 → brukerapi-0.2.4}/test/test_split.py RENAMED
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