Removed unnecessary import checks for scipy, h5py, and zarr

CHANGELOG.md

@@ -7,6 +7,7 @@
 * Added specific error message for single-frame scanimage data [PR #360](https://github.com/catalystneuro/roiextractors/pull/360)
 
 ### Improvements
+* Removed unnecessary import checks for scipy, h5py, and zarr [PR #364](https://github.com/catalystneuro/roiextractors/pull/364)
 
 ### Testing
 

src/roiextractors/extraction_tools.py

@@ -22,21 +22,8 @@
 from packaging import version
 
 
-try:
-    import h5py
-
-    HAVE_H5 = True
-except ImportError:
-    HAVE_H5 = False
-
-
-try:
-    import zarr
-
-    HAVE_ZARR = True
-except ImportError:
-    HAVE_ZARR = False
-
+import h5py
+import zarr
 
 ArrayType = ArrayLike
 PathType = Union[str, Path]
@@ -485,12 +472,9 @@ def write_to_h5_dataset_format(
 
     Raises
     ------
-    AssertionError
-        If h5py is not installed.
     AssertionError
         If neither 'save_path' nor 'file_handle' are given.
     """
-    assert HAVE_H5, "To write to h5 you need to install h5py: pip install h5py"
     assert save_path is not None or file_handle is not None, "Provide 'save_path' or 'file handle'"
 
     if save_path is not None:

src/roiextractors/extractors/caiman/caimansegmentationextractor.py

@@ -8,20 +8,9 @@
 
 from pathlib import Path
 
-try:
-    import h5py
-
-    HAVE_H5PY = True
-except ImportError:
-    HAVE_H5PY = False
-
-try:
-    from scipy.sparse import csc_matrix
-
-    HAVE_SCIPY = True
-except ImportError:
-    HAVE_SCIPY = False
+import h5py
 
+from scipy.sparse import csc_matrix
 import numpy as np
 
 from ...extraction_tools import PathType, get_package
@@ -38,11 +27,8 @@ class CaimanSegmentationExtractor(SegmentationExtractor):
     """
 
     extractor_name = "CaimanSegmentation"
-    installed = HAVE_H5PY and HAVE_SCIPY  # check at class level if installed or not
     is_writable = True
     mode = "file"
-    # error message when not installed
-    installation_mesg = "To use the CaimanSegmentationExtractor install h5py and scipy: \n\n pip install scipy/h5py\n\n"
 
     def __init__(self, file_path: PathType):
         """Initialize a CaimanSegmentationExtractor instance.

src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py

@@ -18,22 +18,15 @@
 from lazy_ops import DatasetView
 
 
-try:
-    import h5py
-
-    HAVE_H5 = True
-except ImportError:
-    HAVE_H5 = False
+import h5py
 
 
 class Hdf5ImagingExtractor(ImagingExtractor):
     """An imaging extractor for HDF5."""
 
     extractor_name = "Hdf5Imaging"
-    installed = HAVE_H5  # check at class level if installed or not
     is_writable = True
     mode = "file"
-    installation_mesg = "To use the Hdf5 Extractor run:\n\n pip install h5py\n\n"  # error message when not installed
 
     def __init__(
         self,

src/roiextractors/extractors/nwbextractors/nwbextractors.py

@@ -14,13 +14,8 @@
 import numpy as np
 from lazy_ops import DatasetView
 
-try:
-    from pynwb import NWBHDF5IO
-    from pynwb.ophys import TwoPhotonSeries, OnePhotonSeries
-
-    HAVE_NWB = True
-except ImportError:
-    HAVE_NWB = False
+from pynwb import NWBHDF5IO
+from pynwb.ophys import TwoPhotonSeries, OnePhotonSeries
 from ...extraction_tools import (
     PathType,
     FloatType,
@@ -42,11 +37,6 @@ def temporary_deprecation_message():
     )
 
 
-def check_nwb_install():
-    """Check if pynwb is installed."""
-    assert HAVE_NWB, "To use the Nwb extractors, install pynwb: \n\n pip install pynwb\n\n"
-
-
 class NwbImagingExtractor(ImagingExtractor):
     """An imaging extractor for NWB files.
 
@@ -55,10 +45,8 @@ class NwbImagingExtractor(ImagingExtractor):
     """
 
     extractor_name = "NwbImaging"
-    installed = HAVE_NWB  # check at class level if installed or not
     is_writable = True
     mode = "file"
-    installation_mesg = "To use the Nwb Extractor run:\n\n pip install pynwb\n\n"  # error message when not installed
 
     def __init__(self, file_path: PathType, optical_series_name: Optional[str] = "TwoPhotonSeries"):
         """Create ImagingExtractor object from NWB file.
@@ -264,7 +252,6 @@ def __init__(self, file_path: PathType):
         file_path: PathType
             .nwb file location
         """
-        check_nwb_install()
         super().__init__()
         file_path = Path(file_path)
         if not file_path.is_file():

src/roiextractors/extractors/sbximagingextractor/sbximagingextractor.py

@@ -16,22 +16,15 @@
 from ...extraction_tools import PathType, ArrayType, raise_multi_channel_or_depth_not_implemented, check_keys
 from ...imagingextractor import ImagingExtractor
 
-try:
-    import scipy.io as spio
-
-    HAVE_Scipy = True
-except ImportError:
-    HAVE_Scipy = False
+import scipy.io as spio
 
 
 class SbxImagingExtractor(ImagingExtractor):
     """Imaging extractor for the Scanbox image format."""
 
     extractor_name = "SbxImaging"
-    installed = HAVE_Scipy  # check at class level if installed or not
     is_writable = True
     mode = "folder"
-    installation_mesg = "To use the Sbx Extractor run:\n\n pip install scipy\n\n"  # error message when not installed
 
     def __init__(self, file_path: PathType, sampling_frequency: Optional[float] = None):
         """Create a SbxImagingExtractor from .mat or .sbx files.

src/roiextractors/extractors/schnitzerextractor/cnmfesegmentationextractor.py

@@ -8,22 +8,10 @@
 
 from pathlib import Path
 
-try:
-    import h5py
-
-    HAVE_H5PY = True
-except ImportError:
-    HAVE_H5PY = False
-
+import h5py
 import numpy as np
 from lazy_ops import DatasetView
-
-try:
-    from scipy.sparse import csc_matrix
-
-    HAVE_SCIPY = True
-except ImportError:
-    HAVE_SCIPY = False
+from scipy.sparse import csc_matrix
 
 from ...extraction_tools import PathType
 from ...multisegmentationextractor import MultiSegmentationExtractor
@@ -39,10 +27,8 @@ class CnmfeSegmentationExtractor(SegmentationExtractor):
     """
 
     extractor_name = "CnmfeSegmentation"
-    installed = HAVE_H5PY  # check at class level if installed or not
     is_writable = False
     mode = "file"
-    installation_mesg = "To use Cnmfe install h5py: \n\n pip install h5py \n\n"  # error message when not installed
 
     def __init__(self, file_path: PathType):
         """Create a CnmfeSegmentationExtractor from a .mat file.
@@ -161,7 +147,6 @@ def write_segmentation(segmentation_object: SegmentationExtractor, save_path: Pa
         AssertionError
             If save_path is not a *.mat file.
         """
-        assert HAVE_SCIPY and HAVE_H5PY, "To use Cnmfe install scipy/h5py: \n\n pip install scipy/h5py \n\n"
         save_path = Path(save_path)
         assert save_path.suffix == ".mat", "'save_path' must be a *.mat file"
         if save_path.is_file():

src/roiextractors/extractors/schnitzerextractor/extractsegmentationextractor.py

@@ -18,13 +18,7 @@
 from lazy_ops import DatasetView
 from packaging import version
 
-try:
-    import h5py
-
-    HAVE_H5PY = True
-except ImportError:
-    HAVE_H5PY = False
-
+import h5py
 
 from ...extraction_tools import PathType, ArrayType
 from ...segmentationextractor import SegmentationExtractor
@@ -39,8 +33,6 @@ class ExtractSegmentationExtractor(ABC):
     """Abstract class that defines which extractor class to use for a given file."""
 
     extractor_name = "ExtractSegmentation"
-    installed = HAVE_H5PY  # check at class level if installed or not
-    installation_mesg = "To use ExtractSegmentationExtractor install h5py: \n\n pip install h5py \n\n"  # error message when not installed
 
     def __new__(
         cls,
@@ -159,11 +151,6 @@ class NewExtractSegmentationExtractor(
     """
 
     extractor_name = "NewExtractSegmentation"
-    installed = HAVE_H5PY  # check at class level if installed or not
-    installation_mesg = (
-        "To use NewExtractSegmentation install h5py: \n\n pip install h5py \n\n"
-        # error message when not installed
-    )
     is_writable = False
     mode = "file"
 
@@ -296,10 +283,8 @@ class LegacyExtractSegmentationExtractor(SegmentationExtractor):
     """
 
     extractor_name = "LegacyExtractSegmentation"
-    installed = HAVE_H5PY  # check at class level if installed or not
     is_writable = False
     mode = "file"
-    installation_mesg = "To use extract install h5py: \n\n pip install h5py \n\n"  # error message when not installed
 
     def __init__(
         self,