[FIX] Spectrum edited name (#365)

* fix output_type params

* add spectrum name edition test cases

* remove strptime dependency on file deserialization

* fix AudioData name deserialization

* force begin-based sorting of data in BaseDataset.data

Author: Gautzilla

src/osekit/core/audio_dataset.py

@@ -165,7 +165,12 @@ def _data_from_dict(cls, dictionary: dict) -> list[AudioData]:
             The list of deserialized ``AudioData`` objects.
 
         """
-        return [AudioData.from_dict(data) for data in dictionary.values()]
+        ads = []
+        for name, value in dictionary.items():
+            ad = AudioData.from_dict(value)
+            ad.name = name
+            ads.append(ad)
+        return ads
 
     @classmethod
     def from_folder(  # noqa: PLR0913

src/osekit/core/base_data.py

@@ -161,18 +161,17 @@ def write(self, folder: Path, *, link: bool = False) -> None:
         """Abstract method for writing data to file."""
 
     @abstractmethod
-    def link(self, folder: Path) -> None:
-        """Abstract method for linking data to a file in a given folder.
+    def link(self, file: Path) -> None:
+        """Abstract method for linking data to a file in a given file.
 
         Linking is intended for data objects that have been written to disk.
         After linking the data to the written file, it will have a single
-        item that matches the File properties.
-        The folder should contain a file named as ``str(self).extension``.
+        item that matches the ``File`` properties.
 
         Parameters
         ----------
-        folder: Path
-            Folder in which is the file to which the ``BaseData`` instance should be linked.
+        file: Path
+            File to which the ``BaseData`` instance should be linked.
 
         """
 

src/osekit/core/base_dataset.py

@@ -130,6 +130,15 @@ def folder(self) -> Path:
             else next(iter(file.path.parent for file in self.files), None)
         )
 
+    @property
+    def data(self) -> list[TData]:
+        """List of Data contained in this Dataset."""
+        return sorted(self._data, key=lambda d: d.begin)
+
+    @data.setter
+    def data(self, data: list[TData]) -> None:
+        self._data = data
+
     @folder.setter
     def folder(self, folder: Path) -> None:
         """Set the folder in which the dataset files might be written.

src/osekit/core/base_file.py

@@ -148,7 +148,10 @@ def from_dict(cls: type[Self], serialized: dict) -> type[Self]:
         path = serialized["path"]
         return cls(
             path=path,
-            strptime_format=TIMESTAMP_FORMATS_EXPORTED_FILES,
+            begin=strptime_from_text(
+                text=serialized["begin"],
+                datetime_template=TIMESTAMP_FORMATS_EXPORTED_FILES,
+            ),
         )
 
     def __hash__(self) -> int:

src/osekit/core/spectro_data.py

@@ -21,9 +21,6 @@
 from pandas import Timedelta
 from scipy.signal import ShortTimeFFT, welch
 
-from osekit.config import (
-    TIMESTAMP_FORMATS_EXPORTED_FILES,
-)
 from osekit.core.audio_data import AudioData
 from osekit.core.base_data import BaseData, TFile
 from osekit.core.spectro_file import SpectroFile
@@ -602,27 +599,25 @@ def write(
             timestamps="_".join(timestamps),
         )
         if link:
-            self.link(folder=folder)
+            self.link(file=folder / f"{self}.npz")
 
-    def link(self, folder: Path) -> None:
-        """Link the ``SpectroData`` to a ``SpectroFile`` in the folder.
+    def link(self, file: Path) -> None:
+        """Link the ``SpectroData`` to a ``SpectroFile``.
 
-        The given folder should contain a file named ``"str(self).npz"``.
         Linking is intended for ``SpectroData`` objects that have already been
         written to disk.
         After linking, the ``SpectroData`` will have a single item with the same
         properties of the target ``SpectroFile``.
 
         Parameters
         ----------
-        folder: Path
-            Folder in which is located the ``SpectroFile`` to which the ``SpectroData``
-            instance should be linked.
+        file: Path
+            File to which the ``SpectroData`` instance should be linked.
 
         """
         file = SpectroFile(
-            path=folder / f"{self}.npz",
-            strptime_format=TIMESTAMP_FORMATS_EXPORTED_FILES,
+            path=file,
+            begin=self.begin,
         )
         self.items = SpectroData.from_files([file]).items
 

src/osekit/core/spectro_dataset.py

@@ -504,18 +504,19 @@ def from_dict(cls, dictionary: dict) -> SpectroDataset:
             )
             for name, sft in dictionary["sft"].items()
         ]
-        sd = [
-            cls.data_cls.from_dict(
+        sds = []
+        for name, params in dictionary["data"].items():
+            sd = cls.data_cls.from_dict(
                 params,
                 sft=next(sft for sft, linked_data in sfts if name in linked_data),
             )
-            for name, params in dictionary["data"].items()
-        ]
+            sd.name = name
+            sds.append(sd)
         scale = dictionary["scale"]
         if dictionary["scale"] is not None:
             scale = Scale.from_dict_value(scale)
         return cls(
-            data=sd,
+            data=sds,
             name=dictionary["name"],
             suffix=dictionary["suffix"],
             folder=Path(dictionary["folder"]),

tests/test_public_api.py

@@ -618,11 +618,11 @@ def test_serialization(
             id="spectro_only",
         ),
         pytest.param(
-            OutputType.SPECTROGRAM,
+            OutputType.SPECTRUM,
             id="spectrum_only",
         ),
         pytest.param(
-            OutputType.SPECTROGRAM,
+            OutputType.SPECTRUM | OutputType.SPECTROGRAM,
             id="both_spectral_flags",
         ),
     ],
@@ -1169,8 +1169,8 @@ def test_prepare_spectro(
 
 
 def test_edit_transform_before_run(
-    tmp_path: pytest.fixture,
-    audio_files: pytest.fixture,
+    tmp_path: Path,
+    audio_files: None,
 ) -> None:
     project = Project(
         folder=tmp_path,
@@ -1181,10 +1181,11 @@ def test_edit_transform_before_run(
     project.build()
 
     transform = Transform(
-        output_type=OutputType.AUDIO | OutputType.SPECTROGRAM,
+        output_type=OutputType.AUDIO | OutputType.SPECTRUM | OutputType.SPECTROGRAM,
         data_duration=project.origin_dataset.duration / 2,
         name="original_transform",
         sample_rate=24_000,
+        v_lim=(0.0, 120.0),
         fft=ShortTimeFFT(win=hamming(1024), hop=1024, fs=24_000),
     )
 
@@ -1205,7 +1206,14 @@ def test_edit_transform_before_run(
     ads.data = new_data
     ads.normalization = new_normalization
 
-    project.run(transform, audio_dataset=ads)
+    # Spectro edits
+    new_v_lim = (50.0, 100.0)
+    sds = project.prepare_spectro(transform=transform, audio_dataset=ads)
+    sds.v_lim = new_v_lim
+    for idx, sd in enumerate(sds.data):
+        sd.name = str(idx)
+
+    project.run(transform, audio_dataset=ads, spectro_dataset=sds)
 
     # New ads name
     assert (project.folder / "data" / "audio" / ads.name).exists()
@@ -1234,6 +1242,10 @@ def test_edit_transform_before_run(
     # Instrument has been edited
     assert output_ads.instrument.end_to_end_db == new_instrument.end_to_end_db
 
+    # Spectro data have been edited
+    assert output_sds.v_lim == new_v_lim
+    assert all(sd.name == str(i) for i, sd in enumerate(output_sds.data))
+
 
 def test_delete_output_dataset(
     tmp_path: pytest.fixture,

tests/test_serialization.py

@@ -280,6 +280,10 @@ def test_audio_dataset_serialization(
         name=name,
     )
 
+    # NO TIMESTAMP IN THE NAME SHOULD STILL BE DESERIALIZED PROPERLY
+    for idx, ad in list(enumerate(ads.data))[::2]:
+        ad.name = str(idx)
+
     assert ads.begin == begin
 
     if type(sample_rate) is list:
@@ -308,10 +312,11 @@ def test_audio_dataset_serialization(
     assert ads.begin == ads2.begin
     assert ads.normalization == ads2.normalization
 
-    assert all(
-        np.array_equal(ad.get_value(), ad2.get_value())
-        for ad, ad2 in zip(ads.data, ads2.data, strict=False)
-    )
+    zipped = zip(ads.data, ads2.data, strict=True)
+
+    assert all(ad1.name == ad2.name for ad1, ad2 in zipped)
+
+    assert all(np.array_equal(ad.get_value(), ad2.get_value()) for ad, ad2 in zipped)
 
 
 @pytest.mark.parametrize(