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Fixes #206

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merged 3 commits into from
Jul 3, 2023
Merged

Fixes #206

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f0ccc6a
fix: bug using -trans with run_multistage_maxfilter.
cgohil8 Jul 3, 2023
b79e104
Fix: broken rhino.utils import.
cgohil8 Jul 3, 2023
4061779
Fix: naming convention if '_raw' is in the original fif file.
cgohil8 Jul 3, 2023
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2 changes: 1 addition & 1 deletion osl/maxfilter/maxfilter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,7 +450,7 @@ def run_multistage_maxfilter(infif, outbase, args):
os.remove(outfif)

# Fixed Args
stage3_args = {'autobad': None}
stage3_args = {'autobad': None, 'force': True}
# User args
for key in ['maxpath', 'scanner', 'ctc', 'cal',
'dryrun', 'overwrite', 'trans', 'outdir']:
Expand Down
14 changes: 6 additions & 8 deletions osl/preprocessing/batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -353,14 +353,12 @@ def write_dataset(dataset, outbase, run_id, overwrite=False):
The saved fif file name
"""

if "preproc_raw" in run_id:
fif_outname = outbase.format(
run_id=run_id.replace("_preproc_raw", ""), ftype="preproc_raw", fext="fif"
)
else:
fif_outname = outbase.format(
run_id=run_id.replace("_raw", ""), ftype="preproc_raw", fext="fif"
)
# Strip "_preproc_raw" or "_raw" from the run id
for string in ["_preproc_raw", "_raw"]:
if string in run_id:
run_id = run_id.replace(string, "")

fif_outname = outbase.format(run_id=run_id, ftype="preproc_raw", fext="fif")
if Path(fif_outname).exists() and not overwrite:
raise ValueError(
"{} already exists. Please delete or do use overwrite=True.".format(fif_outname)
Expand Down
2 changes: 1 addition & 1 deletion osl/preprocessing/osl_wrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ def detect_badchannels(raw, picks, ref_meg="auto", significance_level=0.05):

bdinds = sails.utils.detect_artefacts(
raw.get_data(picks=chinds),
0,
axis=0,
reject_mode="dim",
ret_mode="bad_inds",
gesd_args=gesd_args,
Expand Down
12 changes: 2 additions & 10 deletions osl/source_recon/rhino/polhemus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,7 @@
from mne.io import read_info
from mne.io.constants import FIFF

import os.path as op
import sys
from osl import utils, source_recon
from osl.source_recon.rhino.coreg import get_coreg_filenames

def extract_polhemus_from_info(
Expand Down Expand Up @@ -178,13 +176,7 @@ def delete_headshape_points(recon_dir=None, subject=None, polhemus_headshape_fil
def scatter_headshapes(ax, x, y, z):
# Polhemus-derived headshape points
color, scale, alpha, marker = "red", 8, 0.7, "o"
ax.scatter(x,y,z,
color=color,
marker=marker,
s=scale,
alpha=alpha,
picker=5,
)
ax.scatter(x, y, z, color=color, marker=marker, s=scale, alpha=alpha, picker=5)
plt.draw()

x=list(polhemus_headshape_polhemus[0,:])
Expand Down Expand Up @@ -223,4 +215,4 @@ def on_press(event):
fig.canvas.mpl_connect('pick_event', on_click)
fig.canvas.mpl_connect('key_press_event', on_press)

plt.show()
plt.show()