brukerapi 0.2.2__tar.gz → 0.2.4__tar.gz

{brukerapi-0.2.2/brukerapi.egg-info → brukerapi-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.2
+Version: 0.2.4
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>

brukerapi-0.2.4/brukerapi/config/properties_traj_core.json

@@ -0,0 +1,188 @@
+{
+  "numpy_dtype": [
+    {
+      "cmd": "np.dtype('f8')",
+      "conditions": []
+    }
+  ],
+  "scheme_id": [
+    {
+      "cmd": "'RADIAL'",
+      "conditions": [
+        [
+          "#PULPROG[1:-1]",
+          [
+            "UTE.ppg",
+            "UTE3D.ppg",
+            "IgUTE.ppg",
+            "ZTE.ppg"
+          ]
+        ],
+        [
+          "#ACQ_sw_version",
+          [
+            "<PV 6.0.1>",
+            "<PV 5.1>",
+            "<PV-7.0.0>",
+            "<PV-360.3.0>",
+            "<PV-360.3.1>",
+            "<PV-360.3.2>",
+            "<PV-360.3.3>",
+            "<PV-360.3.4>",
+            "<PV-360.3.5>",
+            "<PV-360.3.6>",
+            "<PV-360.3.7>"
+          ]
+        ]
+      ]
+    },
+    {
+      "cmd": "'SPIRAL'",
+      "conditions": [
+        [
+          "#PULPROG[1:-1]",
+          [
+            "SPIRAL.ppg",
+            "DtiSpiral.ppg"
+          ]
+        ],
+        [
+          "#ACQ_sw_version",
+          [
+            "<PV 6.0.1>",
+            "<PV 5.1>",
+            "<PV-7.0.0>",
+            "<PV-360.3.0>",
+            "<PV-360.3.1>",
+            "<PV-360.3.2>",
+            "<PV-360.3.3>",
+            "<PV-360.3.4>",
+            "<PV-360.3.5>",
+            "<PV-360.3.6>",
+            "<PV-360.3.7>"
+          ]
+        ]
+      ]
+    },
+    {
+      "cmd": "'ZTE'",
+      "conditions": [
+        [
+          "#PULPROG[1:-1]",
+          [
+            "ZTE.ppg"
+          ]
+        ],
+        [
+          "#ACQ_sw_version",
+          [
+            "<PV 6.0.1>",
+            "<PV 5.1>"
+          ]
+        ]
+      ]
+    }
+  ],
+  "traj_type": [
+    {
+      "cmd": "'radial'",
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "RADIAL",
+            "ZTE"
+          ]
+        ]
+      ]
+    },
+    {
+      "cmd": "'spiral'",
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "SPIRAL"
+          ]
+        ]
+      ]
+    }
+  ],
+  "shape_storage": [
+    {
+      "cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro), #NPro)",
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "RADIAL",
+            "ZTE"
+          ]
+        ]
+      ]
+    },
+    {
+      "cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves), #PVM_SpiralNbOfInterleaves)",
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "SPIRAL"
+          ]
+        ]
+      ]
+    }
+  ],
+  "permute": [
+    {
+      "cmd": [
+        0,
+        1,
+        2
+      ],
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "RADIAL",
+            "ZTE",
+            "SPIRAL"
+          ]
+        ]
+      ]
+    }
+  ],
+  "final": [
+    {
+      "cmd": [
+        "#ACQ_dim",
+        "int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro)",
+        "#NPro"
+      ],
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "RADIAL",
+            "ZTE"
+          ]
+        ]
+      ]
+    },
+    {
+      "cmd": [
+        "#ACQ_dim",
+        "int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves)",
+        "#PVM_SpiralNbOfInterleaves"
+      ],
+      "conditions": [
+        [
+          "@scheme_id",
+          [
+            "SPIRAL"
+          ]
+        ]
+      ]
+    }
+  ]
+}

{brukerapi-0.2.2 → brukerapi-0.2.4}/brukerapi/dataset.py

@@ -15,6 +15,7 @@ from .exceptions import (
     DatasetTypeMissmatch,
     FilterEvalFalse,
     IncompleteDataset,
+    InvalidDataset,
     NotADatasetDir,
     ParametersNotLoaded,
     PropertyConditionNotMet,
@@ -269,7 +270,6 @@ class Dataset:
                 if i not in set(os.listdir(str(param_path.parent))):
                     raise IncompleteDataset
 
-
     def load(self):
         """
         Load parameters, properties, schema and data. In case, there is a traj file related to a fid file,
@@ -291,7 +291,7 @@ class Dataset:
 
         self.load_schema()
         self.load_data()
-        # self.load_traj()
+        self.load_traj()
 
     def unload(self):
         """
@@ -401,7 +401,7 @@ class Dataset:
     def unload_properties(self):
         for property in self._properties:
             if hasattr(self, property):
-                delattr(self,property)
+                delattr(self, property)
         self._properties = []
         self._state["load_properties"] = False
 
@@ -565,11 +565,11 @@ class Dataset:
         -------
         1D ndarray containing the full data vector
         """
-        # TODO debug with this
+
         try:
             assert os.stat(str(path)).st_size == np.prod(shape) * dtype.itemsize
         except AssertionError:
-            raise ValueError("Dimension mismatch") from AssertionError
+            raise InvalidDataset("Invalid dataset, dimension mismatch") from AssertionError
 
         return np.array(np.memmap(path, dtype=dtype, shape=shape, order="F")[:])
 
@@ -588,9 +588,10 @@ class Dataset:
 
     def load_traj(self, **kwargs):
         if Path(self.path.parent / "traj").exists() and self.type != "traj":
-            self._traj = Dataset(self.path.parent / "traj", load=False, random_access=self.random_access)
+            self._traj = Dataset(self.path.parent / "traj", load=LOAD_STAGES["empty"])
             self._traj._parameters = self.parameters
-            self._traj._schema = SchemaTraj(self._traj, meta=self.schema._meta, sub_params=self.schema._sub_params, fid=self)
+            self._traj.load_properties()
+            self._traj._schema = SchemaTraj(self._traj)
             self._traj.load_data()
         else:
             self._traj = None

{brukerapi-0.2.2 → brukerapi-0.2.4}/brukerapi/exceptions.py

@@ -248,6 +248,19 @@ class DataNotLoaded(Exception):
         return "DataNotLoaded"
 
 
+class InvalidDataset(Exception):
+    def __init__(self, *args):
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return f"{self.message}"
+        return "Invalid dataset loaded"
+
+
 class TrajNotLoaded(Exception):
     def __init__(self, *args):
         if args:

{brukerapi-0.2.2 → brukerapi-0.2.4}/brukerapi/folders.py

@@ -7,6 +7,7 @@ from .dataset import Dataset
 from .exceptions import (
     FilterEvalFalse,
     IncompleteDataset,
+    InvalidDataset,
     InvalidJcampdxFile,
     JcampdxVersionError,
     NotADatasetDir,
@@ -17,7 +18,7 @@ from .exceptions import (
 )
 from .jcampdx import JCAMPDX
 
-DEFAULT_DATASET_STATE = {"parameter_files": [], "property_files": [], "load": False}
+DEFAULT_DATASET_STATE = {"parameter_files": [], "property_files": [], "load": 3}
 
 
 class Folder:
@@ -220,7 +221,7 @@ class Folder:
             if path.name in self._dataset_index or (path.name.partition(".")[0] in self._dataset_index and "rawdata" in path.name):
                 try:
                     children.append(Dataset(path, **self._dataset_state))
-                except (UnsuportedDatasetType, IncompleteDataset, NotADatasetDir):
+                except (UnsuportedDatasetType, IncompleteDataset, NotADatasetDir, InvalidDataset):
                     continue
 
             try:

{brukerapi-0.2.2 → brukerapi-0.2.4/brukerapi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.2
+Version: 0.2.4
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>

{brukerapi-0.2.2 → brukerapi-0.2.4}/brukerapi.egg-info/SOURCES.txt

@@ -33,4 +33,5 @@ test/test_dataset.py
 test/test_exceptions.py
 test/test_jcampdx.py
 test/test_random_access.py
-test/test_split.py
+test/test_split.py
+test/test_trajectory.py

{brukerapi-0.2.2 → brukerapi-0.2.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "brukerapi"
-version = "0.2.2"
+version = "0.2.4"
 description = "Bruker API"
 authors = [
     { name = "Tomas Psorn", email = "tomaspsorn@isibrno.cz" },

brukerapi-0.2.4/test/test_trajectory.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+import pytest
+
+from brukerapi.dataset import Dataset
+
+TRAJ_PATHS = sorted(Path("test/test_data").rglob("traj"))
+
+
+@pytest.mark.parametrize("traj_path", TRAJ_PATHS, ids=[str(path) for path in TRAJ_PATHS])
+def test_traj_loads_directly(traj_path):
+    dataset = Dataset(traj_path)
+
+    assert dataset.data.shape == dataset.shape_storage
+    assert dataset.data.size > 0
+
+
+@pytest.mark.parametrize("traj_path", TRAJ_PATHS, ids=[str(path) for path in TRAJ_PATHS])
+def test_traj_loads_from_parent_fid(traj_path):
+    parent_path = traj_path.parent / "fid"
+    if not parent_path.exists():
+        parent_path = traj_path.parent / "rawdata.job0"
+
+    dataset = Dataset(parent_path)
+
+    assert dataset.traj.shape == dataset._traj.shape_storage
+    assert dataset.traj.size > 0

brukerapi-0.2.2/brukerapi/config/properties_traj_core.json

@@ -1,109 +0,0 @@
-{
-  "numpy_dtype": [
-    {
-      "cmd": "np.dtype('i4')",
-      "conditions": []
-    }
-  ],
-  "scheme_id": [
-    {
-      "cmd": "'RADIAL'" ,
-      "conditions": [
-        ["#PULPROG[1:-1]",
-          [
-            "UTE.ppg",
-            "UTE3D.ppg",
-            "ZTE.ppg"
-          ]
-        ],
-        ["#ACQ_sw_version",
-          [
-            "<PV 6.0.1>",
-            "<PV 5.1>"
-          ]
-        ]
-      ]
-    },
-    {
-      "cmd": "'SPIRAL'" ,
-      "conditions": [
-        ["#PULPROG[1:-1]",
-          [
-            "SPIRAL.ppg",
-            "DtiSpiral.ppg"
-          ]
-        ],
-        ["#ACQ_sw_version",
-          [
-            "<PV 6.0.1>",
-            "<PV 5.1>"
-          ]
-        ]
-      ]
-    },
-    {
-      "cmd": "'ZTE'" ,
-      "conditions": [
-        ["#PULPROG[1:-1]",
-          [
-            "ZTE.ppg"
-          ]
-        ],
-        ["#ACQ_sw_version",
-          [
-            "<PV 6.0.1>",
-            "<PV 5.1>"
-          ]
-        ]
-      ]
-    }
-  ],
-  "traj_type": [
-    {
-      "cmd": "'radial'",
-      "conditions": [["@scheme_id",["'RADIAL'","'ZTE'"]]]
-    },
-    {
-      "cmd": "'spiral'",
-      "conditions": [["@scheme_id",["SPIRAL"]]]
-    }
-  ],
-  "shape_storage": [
-    {
-      "cmd": "(#ACQ_dim,#ACQ_size[0]//2,#NPro)",
-      "conditions": [["@scheme_id",["RADIAL","ZTE"]]]
-    },
-    {
-      "cmd": "(#ACQ_dim,#ACQ_size[0]//2,#PVM_SpiralNbOfInterleaves)",
-      "conditions": [["@scheme_id",["SPIRAL"]]]
-    }
-  ],
-  "permute": [
-    {
-      "cmd": [
-          0,
-          1,
-          2
-        ],
-      "conditions": [["@scheme_id",["RADIAL","ZTE","SPIRAL"]]]
-    }
-  ],
-  "final": [
-    {
-      "cmd": [
-        "#ACQ_dim",
-        "#ACQ_size[0]//2",
-        "#NPro"
-      ],
-      "conditions": [["@scheme_id",["RADIAL","ZTE"]]]
-    },
-    {
-      "cmd": [
-        "#ACQ_dim",
-        "#ACQ_size[0]//2",
-        "#PVM_SpiralNbOfInterleaves"
-      ],
-      "conditions": [["@scheme_id",["SPIRAL"]]]
-    }
-  ]
-}