brukerapi 0.2.0__tar.gz → 0.2.3__tar.gz

{brukerapi-0.2.0/brukerapi.egg-info → brukerapi-0.2.3}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.0
+Version: 0.2.3
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
+Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
 License: MIT
 Project-URL: Homepage, https://github.com/isi-nmr/brukerapi-python
 Project-URL: Download, https://github.com/isi-nmr/brukerapi-python/releases/latest

{brukerapi-0.2.0 → brukerapi-0.2.3}/brukerapi/config/properties_fid_custom.json

@@ -71,7 +71,7 @@
   "dwell_s": [
     {
         "cmd": "1./ @sw_hz / 2.",
-        "conditions": []
+        "conditions": ["@sw_hz!=0"]
     }
   ],
   "TR": [

{brukerapi-0.2.0 → brukerapi-0.2.3}/brukerapi/dataset.py

@@ -15,6 +15,7 @@ from .exceptions import (
     DatasetTypeMissmatch,
     FilterEvalFalse,
     IncompleteDataset,
+    InvalidDataset,
     NotADatasetDir,
     ParametersNotLoaded,
     PropertyConditionNotMet,
@@ -40,6 +41,12 @@ DEFAULT_STATES = {
         "load": LOAD_STAGES["all"],
         "mmap": False,
     },
+    "fid_proc": {
+        "parameter_files": ["acqp", "method"],
+        "property_files": [Path(__file__).parents[0] / "config/properties_fid_core.json", Path(__file__).parents[0] / "config/properties_fid_custom.json"],
+        "load": LOAD_STAGES["all"],
+        "mmap": False,
+    },
     "2dseq": {
         "parameter_files": ["visu_pars"],
         "property_files": [Path(__file__).parents[0] / "config/properties_2dseq_core.json", Path(__file__).parents[0] / "config/properties_2dseq_custom.json"],
@@ -77,6 +84,15 @@ RELATIVE_PATHS = {
         "AdjStatePerScan": "./AdjStatePerScan",
         "AdjStatePerStudy": "../AdjStatePerStudy",
     },
+    "fid_proc": {
+        "method": "../../method",
+        "acqp": "../../acqp",
+        "subject": "../../../subject",
+        "reco": "./reco",
+        "visu_pars": "./visu_pars",
+        "AdjStatePerScan": "../../AdjStatePerScan",
+        "AdjStatePerStudy": "../../../AdjStatePerStudy",
+    },
     "2dseq": {
         "method": "../../method",
         "acqp": "../../acqp",
@@ -156,7 +172,7 @@ class Dataset:
         containing it. It is possible, to create an empty object using the load switch.
 
         :param path: **str** path to dataset
-        :raise: :UnsuportedDatasetType: In case `Dataset.type` is not in SUPPORTED
+        :raise: :UnsupportedDatasetType: In case `Dataset.type` is not in SUPPORTED
         :raise: :IncompleteDataset: If any of the JCAMP-DX files, necessary to create a Dataset instance is missing
 
         """
@@ -248,8 +264,11 @@ class Dataset:
             raise UnsuportedDatasetType(self.type)
 
         # Check whether all necessary JCAMP-DX files are present
-        if self._state.get("load") >= LOAD_STAGES["parameters"] and not (set(DEFAULT_STATES[self.type]["parameter_files"]) <= set(os.listdir(str(self.path.parent)))):
-            raise IncompleteDataset
+        if self._state.get("load") >= LOAD_STAGES["parameters"]:
+            for i in DEFAULT_STATES[self.type]["parameter_files"]:
+                param_path = self.path.parent / RELATIVE_PATHS[self.type][i]
+                if i not in set(os.listdir(str(param_path.parent))):
+                    raise IncompleteDataset
 
     def load(self):
         """
@@ -381,7 +400,8 @@ class Dataset:
 
     def unload_properties(self):
         for property in self._properties:
-            delattr(self, property)
+            if hasattr(self, property):
+                delattr(self, property)
         self._properties = []
         self._state["load_properties"] = False
 
@@ -486,7 +506,7 @@ class Dataset:
         """
         Load the schema for given data set.
         """
-        if self.type == "fid":
+        if self.type in ["fid", "fid_proc"]:
             self._schema = SchemaFid(self)
         elif self.type == "2dseq":
             self._schema = Schema2dseq(self)
@@ -545,11 +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")[:])
 

{brukerapi-0.2.0 → brukerapi-0.2.3}/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-0.2.0 → brukerapi-0.2.3}/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-0.2.0 → brukerapi-0.2.3}/brukerapi/schemas.py

@@ -10,6 +10,20 @@ config_paths = {"core": Path(__file__).parents[0] / "config", "custom": Path(__f
 # properties required for loading of the data array for each dataset type
 REQUIRED_PROPERTIES = {
     "fid": ["numpy_dtype", "channels", "block_size", "acq_lenght", "scheme_id", "block_count", "encoding_space", "permute", "k_space", "encoded_dim", "shape_storage", "dim_type"],
+    "fid_proc": [
+        "numpy_dtype",
+        "channels",
+        "block_size",
+        "acq_lenght",
+        "scheme_id",
+        "block_count",
+        "encoding_space",
+        "permute",
+        "k_space",
+        "encoded_dim",
+        "shape_storage",
+        "dim_type"
+    ],
     "2dseq": [
         "pv_version",
         "numpy_dtype",

{brukerapi-0.2.0 → brukerapi-0.2.3/brukerapi.egg-info}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.0
+Version: 0.2.3
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
+Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
 License: MIT
 Project-URL: Homepage, https://github.com/isi-nmr/brukerapi-python
 Project-URL: Download, https://github.com/isi-nmr/brukerapi-python/releases/latest

{brukerapi-0.2.0 → brukerapi-0.2.3}/pyproject.toml

@@ -4,12 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "brukerapi"
-version = "0.2.0"
+version = "0.2.3"
 description = "Bruker API"
 authors = [
     { name = "Tomas Psorn", email = "tomaspsorn@isibrno.cz" },
     { name = "Jiri Vitous", email = "vitous@isibrno.cz" },
 ]
+maintainers = [{ name = "Jiri Vitous", email = "vitous@isibrno.cz" }]
+
 license = { text = "MIT" }
 readme = "README.rst"
 requires-python = ">=3.8"
@@ -18,6 +20,8 @@ dependencies = [
     "numpy>=1.26.0; python_version>='3.9'",
     "pyyaml",
 ]
+
+
 urls = { "Homepage" = "https://github.com/isi-nmr/brukerapi-python", "Download" = "https://github.com/isi-nmr/brukerapi-python/releases/latest" }
 
 [project.scripts]