New versioning system and a bunch of other shit

bip/VERSION

+1.8
\ No newline at end of file

bip/__init__.py

+import os.path as op
+
+basedir     = op.dirname(__file__)
+__version__ = open(op.join(basedir, 'VERSION')).read()

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
 

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)
 

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),

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)
 

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")

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]

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.
+

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)

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)

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)

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)

setup.py

+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,