Future proofing imports (#273)

osl/report/preproc_report.py

@@ -22,11 +22,15 @@
 from jinja2 import Template
 from tabulate import tabulate
 from mne.channels.channels import channel_type
-from scipy.ndimage.filters import uniform_filter1d
 from matplotlib.lines import Line2D
 from matplotlib.patches import Rectangle
 from pathlib import Path
 
+try:
+    from scipy.ndimage import uniform_filter1d
+except ImportError:
+    from scipy.ndimage.filters import uniform_filter1d
+
 from ..utils import process_file_inputs, validate_outdir
 from ..utils.logger import log_or_print
 from ..preprocessing import (

osl/report/src_report.py

@@ -138,7 +138,7 @@ def save_extra_funcs(extra_funcs, reportdir):
         Path to saved text file.
     """
 
-    if reportdir is not None:
+    if reportdir is not None and extra_funcs is not None:
         fpath = reportdir / 'extra_funcs.txt'
         with(open(fpath, 'w')) as file:
             [print(f"{inspect.getsource(func)}\n\n", file=file) for func in extra_funcs]

osl/source_recon/beamforming.py

@@ -12,9 +12,6 @@
 import matplotlib.pyplot as plt
 import mne
 from mne import read_forward_solution, Covariance, compute_covariance, compute_raw_covariance
-from mne.io.meas_info import _simplify_info
-from mne.io.pick import pick_channels_cov, pick_info
-from mne.io.proj import make_projector
 from mne.rank import compute_rank
 from mne.minimum_norm.inverse import _check_depth, _prepare_forward, _get_vertno
 from mne.source_estimate import _get_src_type
@@ -39,6 +36,16 @@
 )
 from mne.utils import logger as mne_logger
 
+try:
+    from mne._fiff.meas_info import _simplify_info
+    from mne._fiff.pick import pick_channels_cov, pick_info
+    from mne._fiff.proj import make_projector
+except ImportError:
+    # Depreciated in mne 1.6
+    from mne.io.meas_info import _simplify_info
+    from mne.io.pick import pick_channels_cov, pick_info
+    from mne.io.proj import make_projector
+
 from osl.source_recon import rhino
 from osl.source_recon.rhino import utils as rhino_utils
 from osl.utils.logger import log_or_print

osl/source_recon/rhino/coreg.py

@@ -20,8 +20,19 @@
 from mne.viz.backends.renderer import _get_renderer
 from mne.transforms import write_trans, read_trans, apply_trans, _get_trans, combine_transforms, Transform, rotation, invert_transform
 from mne.forward import _create_meg_coils
-from mne.io import _loc_to_coil_trans, read_info, read_raw, RawArray
-from mne.io.pick import pick_types
+from mne.io import read_info, read_raw, RawArray
+
+try:
+    from mne import pick_types
+except ImportError:
+    # Depreciated in mne 1.6
+    from mne.io.pick import pick_types
+
+try:
+    from mne._fiff.tag import _loc_to_coil_trans
+except ImportError:
+    # Depreciated in mne 1.6
+    from mne.io import _loc_to_coil_trans
 
 from fsl import wrappers as fsl_wrappers
 
@@ -604,7 +615,7 @@ def coreg_display(
 
         meg_picks = pick_types(info, meg=True, ref_meg=False, exclude=())
 
-        coil_transs = [_loc_to_coil_trans(info["chs"][pick]["loc"]) for pick in meg_picks ]
+        coil_transs = [_loc_to_coil_trans(info["chs"][pick]["loc"]) for pick in meg_picks]
         coils = _create_meg_coils([info["chs"][pick] for pick in meg_picks], acc="normal")
 
         meg_rrs, meg_tris, meg_sensor_locs, meg_sensor_oris = (list(), list(), list(), list())

osl/source_recon/rhino/forward_model.py

@@ -17,7 +17,12 @@
 from mne.io import read_info
 from mne.io.constants import FIFF
 from mne.surface import read_surface, write_surface
-from mne.source_space import _make_volume_source_space, _complete_vol_src
+
+try:
+    from mne.source_space import _make_volume_source_space, _complete_vol_src
+except ImportError:
+    # Depreciated in mne 1.6
+    from mne.source_space._source_space import _make_volume_source_space, _complete_vol_src
 
 import osl.source_recon.rhino.utils as rhino_utils
 from osl.source_recon.rhino import get_coreg_filenames

osl/utils/file_handling.py

@@ -71,7 +71,7 @@ def process_file_inputs(inputs):
                 for row in inputs:
                     infiles.append(sanitise_filepath(row[0]))
                     outnames.append(row[1])
-            elif isinstance(inputs[0], mne.io.fiff.raw.Raw):
+            elif isinstance(inputs[0], mne.io.Raw):
                 # We have a list of MNE objects
                 infiles = infiles
                 check_paths = False
@@ -125,7 +125,7 @@ def find_run_id(infile, preload=True):
     # the fif option for everything except BTI scans? They're basically the
     # same now.
 
-    if isinstance(infile, mne.io.fiff.raw.Raw):
+    if isinstance(infile, mne.io.Raw):
         infile = infile.filenames[0]
 
     if os.path.split(infile)[1] == 'c,rfDC':

osl/utils/opm.py

@@ -11,10 +11,15 @@
 import numpy as np
 
 import mne
-from mne.io import _coil_trans_to_loc
 from mne.io.constants import FIFF
 from mne.transforms import Transform, apply_trans
 
+try:
+    from mne._fiff.tag import _coil_trans_to_loc
+except ImportError:
+    # Depreciated in mne 1.6
+    from mne.io import _coil_trans_to_loc
+
 import pandas as pd
 import scipy
 
@@ -234,10 +239,9 @@ def correct_mri(smri_file, smri_fixed_file):
 
     return sform_std
 
-#########################################################################
-
 # -------------------------------------------------------------
 # %% Debug and plotting code for checking sensor locs and oris
+
 if False:
 
     from mne.io.pick import pick_types