diff --git a/bip/VERSION b/bip/VERSION
new file mode 100644
index 0000000000000000000000000000000000000000..468437494697b8d457e2b251edb3e76047d0321b
--- /dev/null
+++ b/bip/VERSION
@@ -0,0 +1 @@
+1.8
\ No newline at end of file
diff --git a/bip/__init__.py b/bip/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..83b51e1ed45def769589beb2535ea4606e3f10d7
--- /dev/null
+++ b/bip/__init__.py
@@ -0,0 +1,4 @@
+import os.path as op
+
+basedir = op.dirname(__file__)
+__version__ = open(op.join(basedir, 'VERSION')).read()
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
index a31994db9cc8b018ef19e33ba3cbc2051fb0d559..d0b6a7f12f6b6160ef886ece505f1e6956b8d42c 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
@@ -14,7 +14,7 @@ import os
import logging
import nibabel as nib
from fsl import wrappers
-from pipe_tree import In, Out, Ref
+from pipe_tree import In, Out, Ref, Var
from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
@@ -24,7 +24,8 @@ def run(ctx,
TBSS_prefix: Ref,
aptx_txt_prefix: Ref,
tmp_dir: Ref,
- aptx_tract_tmp: In(no_iter=True),
+ aptx_tract_tmp: In,
+ autoptx_tract: Var(no_iter=True),
IDP_diff_autoPtx: Out):
with redirect_logging('IDP_diff_autoPtx', outdir=logs_dir),\
@@ -37,7 +38,7 @@ def run(ctx,
result = ""
# TODO: See if it is possible to generate the aptx_tract_tmp files here
- wrappers.fslmerge(autoPtx_all, *list(aptx_tract_tmp.data))
+ wrappers.fslmerge("t", autoPtx_all, *list(aptx_tract_tmp.data))
tractnorm = wrappers.fslstats(autoPtx_all, t=True).m.run()
for suffix in ['FA','L1','L2','L3','MO','MD','ICVF','OD','ISOVF']:
@@ -59,7 +60,7 @@ def run(ctx,
with open(APTX_file, 'wt', encoding="utf-8") as f:
f.write(f'{cad}\n')
- result += cad
+ result += " " + cad
else:
result += " " + result_NaN
diff --git a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
index 27da52e57324f75f99a7b97823506aadd0004405..d56aab7ca067ac5241ee7eeaec7b492f640ffbfd 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
@@ -76,20 +76,20 @@ def run(ctx,
N_tfMRI_featquery_5a_dir = tfMRI_featquery_5a_dir.replace(tfMRI_feat,"")
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope1, N_tfMRI_zstat1],
+ wrappers.featquery(featdirs=[tfMRI_feat],
+ stats=[N_tfMRI_cope1, N_tfMRI_zstat1],
outputRootName=N_tfMRI_featquery_1_dir,
mask=group_mask_1)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope2, N_tfMRI_zstat2],
+ wrappers.featquery(featdirs=[tfMRI_feat],
+ stats=[N_tfMRI_cope2, N_tfMRI_zstat2],
outputRootName=N_tfMRI_featquery_2_dir,
mask=group_mask_2)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
+ wrappers.featquery(featdirs=[tfMRI_feat],
+ stats=[N_tfMRI_cope5, N_tfMRI_zstat5],
outputRootName=N_tfMRI_featquery_5_dir,
mask=group_mask_5)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
+ wrappers.featquery(featdirs=[tfMRI_feat],
+ stats=[N_tfMRI_cope5, N_tfMRI_zstat5],
outputRootName=N_tfMRI_featquery_5a_dir,
mask=group_mask_5a)
diff --git a/bip/pipelines/IDPs_gen/IDPs_gen.py b/bip/pipelines/IDPs_gen/IDPs_gen.py
index ae8d60abbd87b750998ad00b224f55046c65aba8..52e4e13174e3f36d8d6061bf4be90aa29178e760 100755
--- a/bip/pipelines/IDPs_gen/IDPs_gen.py
+++ b/bip/pipelines/IDPs_gen/IDPs_gen.py
@@ -27,7 +27,7 @@ from bip.pipelines.IDPs_gen import IDP_func_TSNR
from bip.pipelines.IDPs_gen import IDP_func_task_activation
from bip.pipelines.IDPs_gen import IDP_diff_eddy_outliers
from bip.pipelines.IDPs_gen import IDP_diff_TBSS
-#from bip.pipelines.IDPs_gen import IDP_diff_autoPtx
+from bip.pipelines.IDPs_gen import IDP_diff_autoPtx
from bip.pipelines.IDPs_gen import IDPs_generator
log = logging.getLogger(__name__)
@@ -109,10 +109,10 @@ def add_to_pipeline(ctx, pipe, tree, targets):
kwargs={'ctx' : ctx})
targets.append('IDP_diff_TBSS')
- #pipe(IDP_diff_autoPtx.run,
- # submit=dict(jobtime=200, name="BIP_IDP_diff_autoPtx_"+ subj),
- # kwargs={'ctx' : ctx})
- #targets.append('IDP_diff_autoPtx')
+ pipe(IDP_diff_autoPtx.run,
+ submit=dict(jobtime=200, name="BIP_IDP_diff_autoPtx_"+ subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_diff_autoPtx')
pipe(IDP_subject_COG_table.run,
submit=dict(jobtime=200, name="BIP_IDP_subject_COG_table_" + subj),
diff --git a/bip/pipelines/dMRI_diff/diff_eddy.py b/bip/pipelines/dMRI_diff/diff_eddy.py
index 9baeee980e10e7fba8bcd15b018f94f4356a8ea7..a4d286a22eef1c02dd90352c411d1d9c57c3b02c 100755
--- a/bip/pipelines/dMRI_diff/diff_eddy.py
+++ b/bip/pipelines/dMRI_diff/diff_eddy.py
@@ -42,7 +42,8 @@ def run(ctx,
eddy_data: Out,
eddy_outlier_report: Out):
- with redirect_logging('diff_eddy', outdir=logs_dir):
+ #TODO: Do the __name__ for everything
+ with redirect_logging(__name__, outdir=logs_dir):
# Creates links
# TODO: These links are NOT relative. This may cause future problems.
@@ -55,7 +56,6 @@ def run(ctx,
if not os.path.exists(eddy_nodif_brain_mask_ud):
os.symlink(src="../../../" + fieldmap_mask_ud, dst=eddy_nodif_brain_mask_ud)
- # Generation of FSF file
copyfile(src=AP_bval, dst=eddy_bvals)
copyfile(src=AP_bvec, dst=eddy_bvecs)
diff --git a/bip/pipelines/dMRI_diff/diff_tbss.py b/bip/pipelines/dMRI_diff/diff_tbss.py
index 82dfce2270664e1eeb1faf53517f163ad1097dd0..ce77c626a5a2dd9bc3f1ca70ebad911c5c2407e3 100755
--- a/bip/pipelines/dMRI_diff/diff_tbss.py
+++ b/bip/pipelines/dMRI_diff/diff_tbss.py
@@ -59,7 +59,7 @@ def run(ctx,
TBSS_FA_to_MNI_warp_s2 = tmp_dir + '/FA_to_MNI_warp_s2.nii.gz'
# Creates links
- # TODO: These links are NOT relative. This may cause future problems.
+ # TODO: Do the cool OS.PATH.RELPATH
if not os.path.exists(TBSS_FA):
os.symlink(src="../../../" + FA, dst=TBSS_FA)
if not os.path.exists(TBSS_MNI):
@@ -159,5 +159,4 @@ def run(ctx,
wrappers.fslmaths(d_output).mas(TBSS_mean_FA_skeleton_mask).run(d_output_skel)
mean = wrappers.fslstats( d_output_skel, K=atlas).M.run()
- with open(d_output_txt, 'wt', encoding="utf-8") as f:
- f.write(f'{mean}')
+ np.savetxt(d_output_txt, mean, fmt="%0.8f")
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
index cef087bd17c1fdb79bd97dec3ea55ebfcd2456fb..745eb55bb8c84cc1c333342705c787f875855f9a 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
@@ -75,7 +75,7 @@ def run(ctx,
x1,y1,z1 = np.where(B0_AP_corr_tmp_imgf==0)
x2,y2,z2 = np.where(B0_PA_corr_tmp_imgf==0)
- #For AP voxels with 0 value,, get the values in PA (And viceversa)
+ #For AP voxels with 0 value, get the values in PA (And viceversa)
B0_AP_fixed_tmp_imgf = B0_AP_corr_tmp_imgf
B0_PA_fixed_tmp_imgf = B0_PA_corr_tmp_imgf
B0_AP_fixed_tmp_imgf[x1,y1,z1] = B0_PA_corr_tmp_imgf[x1,y1,z1]
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
index f6b2084919bf80dd3634d51e9a35fe5cbe612a57..0473ec10efd07bc6855239c427f86c1032c3bdc3 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
@@ -69,9 +69,11 @@ def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
scores[i,j] = corr
scores[j,i] = corr
- final_scores = np.zeros(N)
- for i in range(N):
- final_scores[i]=np.sum(scores[:,i]) / (N - 1)
+ # TODO: Do in one line
+ #final_scores = np.zeros(N)
+ #for i in range(N):
+ # final_scores[i]=np.sum(scores[:,i]) / (N - 1)
+ final_scores = np.sum(scores, axis=1) / (N - 1)
best_ind = final_scores.argmax()
best_score = final_scores[best_ind]
@@ -201,3 +203,5 @@ def run(ctx,
if (Zslices % 2) != 0:
wrappers.fslroi(B0_AP_PA, B0_AP_PA, 0, -1, 0, -1, 0, Zslices -1)
+ # TODO: Discuss this with Jesper.
+
diff --git a/bip/pipelines/struct_FS/FS_get_IDPs.py b/bip/pipelines/struct_FS/FS_get_IDPs.py
index df9944d0b2196fadb334dd469eb2e4e47ef94c2a..3a14ccf4e66f4078c34c6066b3c94741aa8741c8 100755
--- a/bip/pipelines/struct_FS/FS_get_IDPs.py
+++ b/bip/pipelines/struct_FS/FS_get_IDPs.py
@@ -517,6 +517,7 @@ def bb_FS_get_IDPs(ctx, env):
dataDir = subjectDir + '/data/'
headersDir = subjectDir + '/headers/'
+ #TODO: Raise an exception
if not os.path.isdir(subjectDir):
print("Error: FreeSurfer has not been run on this subject")
sys.exit(-1)
diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index d45c0485b94c5fced7a150c8b0f9b3e8476dd72a..a4bb840b7b3d0993a7d37c1fab21f36afe86f9de 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/bip/pipelines/struct_FS/FS_proc.py
@@ -32,6 +32,7 @@ def run(ctx,
if os.path.exists(FreeSurfer_dir):
shutil.rmtree(FreeSurfer_dir)
+ #TODO: SUBJECTS_DIR can be an argument of freesurfer instead of this craps
env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
T1_path = os.getcwd() + "/" + T1_unbiased
@@ -39,16 +40,13 @@ def run(ctx,
cmd = 'recon-all -all -s FreeSurfer -i ' + T1_path
- if os.path.exists(T2_FLAIR_unbiased):
+ #TODO: Do this for all cases of os.path.exits (all optional things)
+ if T2_FLAIR_unbiased is not None and os.path.exists(T2_FLAIR_unbiased):
cmd += " -FLAIR " + T2_path + " -FLAIRpial"
- output = run_command(log, cmd, env)
-
- log.info(output)
-
- if os.path.exists(fsaverage):
- os.unlink(fsaverage)
-
- #ext_wrappers.recon_all(subjects_dir=os.getcwd(),
- # directive="all", subjid="FreeSurfer",
- # infile=T1_unbiased, FLAIR=opt_T2_FLAIR)
+ try:
+ output = run_command(log, cmd, env=env)
+ log.info(output)
+ finally:
+ if os.path.exists(fsaverage):
+ os.unlink(fsaverage)
diff --git a/bip/pipelines/struct_T1/T1_first.py b/bip/pipelines/struct_T1/T1_first.py
index 8b1ca75033689c234d1adf751c2983e66375d886..71f15d69f89a704b878513a3052c46ae82749b17 100755
--- a/bip/pipelines/struct_T1/T1_first.py
+++ b/bip/pipelines/struct_T1/T1_first.py
@@ -37,6 +37,8 @@ def run(ctx,
output=T1_first_prefix, b=True)
for f in glob.glob(T1_first_prefix + "-*_first*.nii.gz"):
- os.remove(f)
+ if os.path.exists(f):
+ os.remove(f)
for f in glob.glob(T1_first_prefix + "-*_corr*.nii.gz"):
- os.remove(f)
+ if os.path.exists(f):
+ os.remove(f)
diff --git a/bip/utils/log_utils.py b/bip/utils/log_utils.py
index 2666ef006fa19a4423ba74879d6dbbd216bdafed..1abf843c9848cdf7274fd57e55b8ea1b79e4a720 100755
--- a/bip/utils/log_utils.py
+++ b/bip/utils/log_utils.py
@@ -22,13 +22,13 @@ from subprocess import check_output
from fsl import wrappers
-#def run_command(logger, command, **kwargs): This fails
-def run_command(logger, command, env):
+def run_command(logger, command, **kwargs): This fails
+#def run_command(logger, command, env):
try:
logger.info(command.strip())
# This fails
- #job_output = check_output(command,shell=True,**kwargs).decode('UTF-8')
- job_output = check_output(command,shell=True,env=env).decode('UTF-8')
+ job_output = check_output(command,shell=True,**kwargs).decode('UTF-8')
+ #job_output = check_output(command,shell=True,env=env).decode('UTF-8')
logger.info('Output: \t' + job_output.strip())
except Exception as e:
@@ -36,7 +36,7 @@ def run_command(logger, command, env):
logger.error('Exception type: \t' + str(type(e)))
logger.error('Exception args: \t' + str(e.args))
logger.error('Exception message: \t' + str(e))
- job_output = ""
+ raise
return job_output.strip()
@@ -136,14 +136,11 @@ def redirect_logging(name, outdir='.', level=logging.INFO, verbose=True):
if getattr(log, 'handler', None):
log.addHandler(log.handler)
-
@contextlib.contextmanager
def tempdir(dir_name):
+ ''' This is meant to remove the temp directory only if the calling function
+ succeeds.
+ '''
os.makedirs(dir_name, exist_ok=True)
yield dir_name
- for file_name in os.listdir(dir_name):
- file_path = os.path.join(dir_name, file_name)
- try:
- shutil.rmtree(file_path)
- except OSError:
- os.remove(file_path)
+ shutil.rmtree(dir_name)
diff --git a/setup.py b/setup.py
index 8bc548eac6e1396aaf98513c0f1e49b9e5af8fb3..1cd3ee64cc721c3786cc5dc8b2b90d484cb11025 100644
--- a/setup.py
+++ b/setup.py
@@ -1,9 +1,14 @@
+import os.path as op
from setuptools import setup,find_packages
+
with open('requirements.txt', 'rt') as f:
install_requires = [l.strip() for l in f.readlines()]
+basedir = op.dirname(__file__)
+version = open(op.join(basedir, 'bip', 'VERSION')).read().strip()
+
setup(name='bip',
- version='1.0.0',
+ version=version,
description='Brain Imaging Pipeline',
author='Fidel Alfaro Almagro',
install_requires=install_requires,