antspymm 1.3.4__py3-none-any.whl → 1.3.6__py3-none-any.whl

antspymm/mm.py

@@ -3451,6 +3451,9 @@ def dipy_dti_recon(
         bvals = bvalsfn.copy()
         bvecs = bvecsfn.copy()
 
+    if bvals.max() < 1.0:
+        raise ValueError("DTI recon error: maximum bvalues are too small.")
+
     b0_idx = segment_timeseries_by_bvalue( bvals )['highermeans']
 
     b0 = ants.slice_image( image, axis=3, idx=b0_idx[0] )
@@ -7975,16 +7978,20 @@ def mm_csv(
                 hier['dataframes'], identifier=None )
         t1wide.to_csv( hierfn + 'mmwide.csv' )
     ################# read the hierarchical data ###############################
+    # over-write the rbp data with a consistent and recent approach ############
+    myx = antspyt1w.inspect_raw_t1( t1, hierfn + 'rbp' , option='both' )
+    myx['brain'].to_csv( hierfn + 'rbp.csv', index=False )
+    myx['brain'].to_csv( hierfn + 'rbpbrain.csv', index=False )
+    del myx
     hier = antspyt1w.read_hierarchical( hierfn )
-    if exists( hierfn + 'mmwide.csv' ) :
-        t1wide = pd.read_csv( hierfn + 'mmwide.csv' )
-    elif not testloop:
-        t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
-                hier['dataframes'], identifier=None )
-    if t1wide['resnetGrade'].iloc[0] < 0.35:
-        rgrade = str( t1wide['resnetGrade'].iloc[0] )
+    t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
+        hier['dataframes'], identifier=None )
+    rgrade = str( t1wide['resnetGrade'].iloc[0] )
+    if t1wide['resnetGrade'].iloc[0] < 0.20:
         warnings.warn('T1w quality check indicates failure: ' + rgrade + " will not process." )
         return
+    else:
+        print('T1w quality check indicates success: ' + rgrade + " will process." )
 
     if srmodel_T1 is not False :
         hierfntest = hierfnSR + 'mtl.csv'
@@ -8079,6 +8086,8 @@ def mm_csv(
                 print( 'example image name is : '  )
                 print( myimgsr )
             if overmodX == 'NM2DMT':
+                dowrite = True
+                visualize = True
                 subjectpropath = os.path.dirname( mydoc['outprefix'] )
                 if verbose:
                     print("subjectpropath is")
@@ -8138,16 +8147,17 @@ def mm_csv(
                         print(f"antspymmerror occurred while processing {overmodX}: {e}")
                         pass
                     if not test_run:
-                        write_mm( output_prefix=mymm, mm=tabPro, mm_norm=normPro, t1wide=None, separator=mysep )
-                        nmpro = tabPro['NM']
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                    if visualize:
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                        ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
-                        mysl = range( nmpro['NM_avg_cropped'].shape[2] )
-                        ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
+                        if dowrite:
+                            write_mm( output_prefix=mymm, mm=tabPro,
+                                mm_norm=normPro, t1wide=None, separator=mysep )
+                        if visualize :
+                            nmpro = tabPro['NM']
+                            mysl = range( nmpro['NM_avg'].shape[2] )
+                            ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
+                            mysl = range( nmpro['NM_avg_cropped'].shape[2] )
+                            ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
             else :
                 if len( myimgsr ) > 0:
                     dowrite=False
@@ -9544,6 +9554,7 @@ def blind_image_assessment(
         image_reference = ants.image_clone( image )
     ntimepoints = 1
     bvalueMax=None
+    bvecnorm=None
     if image_reference.dimension == 4:
         ntimepoints = image_reference.shape[3]
         if "DTI" in image_filename:
@@ -9556,6 +9567,8 @@ def blind_image_assessment(
             if exists( bval_name ) and exists( bvec_name ):
                 bvals, bvecs = read_bvals_bvecs( bval_name , bvec_name  )
                 bvalueMax = bvals.max()
+                bvecnorm = np.linalg.norm(bvecs,axis=1).reshape( bvecs.shape[0],1 )
+                bvecnorm = bvecnorm.max()
         else:
             image_b0 = ants.get_average_of_timeseries( image_reference ).iMath("Normalize")
     else:
@@ -9721,11 +9734,11 @@ def blind_image_assessment(
             noizlevel, snrref, cnrref, psnrref, ssimref, mymi, asym_err, myevr, msk_vol, 
             spc[0], spc[1], spc[2],org[0], org[1], org[2], 
             image.shape[0], image.shape[1], image.shape[2], ntimepoints, 
-            jjj, modality, mriseries, mrimfg, mrimodel, MagneticFieldStrength, mriSAR, PixelBandwidth, BandwidthPerPixelPhaseEncode, bvalueMax ]], 
+            jjj, modality, mriseries, mrimfg, mrimodel, MagneticFieldStrength, mriSAR, PixelBandwidth, BandwidthPerPixelPhaseEncode, bvalueMax, bvecnorm ]], 
             columns=[
                 'filename', 
                 'dimensionality',
-                'noise', 'snr', 'cnr', 'psnr', 'ssim', 'mi', 'reflection_err', 'EVR', 'msk_vol', 'spc0','spc1','spc2','org0','org1','org2','dimx','dimy','dimz','dimt','slice','modality', 'mriseries', 'mrimfg', 'mrimodel', 'mriMagneticFieldStrength', 'mriSAR', 'mriPixelBandwidth', 'mriPixelBandwidthPE', 'dti_bvalueMax' ])
+                'noise', 'snr', 'cnr', 'psnr', 'ssim', 'mi', 'reflection_err', 'EVR', 'msk_vol', 'spc0','spc1','spc2','org0','org1','org2','dimx','dimy','dimz','dimt','slice','modality', 'mriseries', 'mrimfg', 'mrimodel', 'mriMagneticFieldStrength', 'mriSAR', 'mriPixelBandwidth', 'mriPixelBandwidthPE', 'dti_bvalueMax', 'dti_bvecnorm' ])
         outdf = pd.concat( [outdf, df ], axis=0, ignore_index=False )
         if verbose:
             print( outdf )
@@ -10893,6 +10906,7 @@ def aggregate_antspymm_results_sdf(
     splitsep='-',
     idsep='-',
     wild_card_modality_id=False,
+    second_split=False,
     verbose=False ):
     """
     Aggregate ANTsPyMM results from the specified study data frame and store the aggregated results in a new data frame.  This assumes data is organized on disk 
@@ -10911,6 +10925,7 @@ def aggregate_antspymm_results_sdf(
     - idsep (str): the separator used to partition subjectid date and imageid 
         for example, if idsep is - then we have subjectid-date-imageid
     - wild_card_modality_id (bool): keep if False for safer execution
+    - second_split (bool): this is a hack that will split the imageID by . and keep the first part of the split; may be needed when the input filenames contain .
     - verbose : boolean
 
     Note:
@@ -10992,12 +11007,24 @@ def aggregate_antspymm_results_sdf(
         myproj = str(df[project_col].iloc[x])
         mydate = str(df[date_col].iloc[x])
         myid = str(df[image_col].iloc[x])
+        if second_split:
+            myid = myid.split(".")[0]
         path_template = base_path + "/" + myproj +  "/" + sid + "/" + mydate + '/' + hiervariable + '/' + str(myid) + "/"
         hierfn = sorted(glob( path_template + "*" + hiervariable + "*wide.csv" ) )
+        if len( hierfn ) == 0:
+            print( hierfn )
+            print( path_template )
+            print( myproj )
+            print( sid )
+            print( mydate ) 
+            print( myid )
         if len( hierfn ) > 0:
             keep[x]=True
 
-    df=df[keep]
+    # df=df[keep]
+    if df.shape[0] == 0:
+        warnings.warn("input data frame shape is filtered down to zero")
+        return df
 
     if not df.index.is_unique:
         warnings.warn("data frame does not have unique indices.  we therefore reset the index to allow the function to continue on." )
@@ -11030,7 +11057,8 @@ def aggregate_antspymm_results_sdf(
         myproj = str(df[project_col].iloc[x])
         mydate = str(df[date_col].iloc[x])
         myid = str(df[image_col].iloc[x])
-        myt1id = myid
+        if second_split:
+            myid = myid.split(".")[0]
         if verbose:
             print( myfn )
             print( temp )
@@ -11090,7 +11118,6 @@ def aggregate_antspymm_results_sdf(
                     nlarge = len(t1wfn)
                     t1wfn = find_most_recent_file( t1wfn )
                     warnings.warn("there are " + str( nlarge ) + " number of wide fns with search path " + modsearch + " we take the most recent of these " + t1wfn[0] )
-#                    raise ValueError("there are " + str( len( t1wfn ) ) + " number of wide fns with search path " + modsearch )
                 if len( t1wfn ) == 1:
                     if verbose:
                         print(t1wfn)
@@ -11108,9 +11135,11 @@ def aggregate_antspymm_results_sdf(
             hdf.index = subdf.index.copy()
             subdf = pd.concat( [subdf,hdf], axis=1, ignore_index=False)
             dfout = pd.concat( [dfout,subdf], axis=0, ignore_index=False )
-    badnames = get_names_from_data_frame( ['Unnamed'], dfout )
-    dfout=dfout.drop(badnames, axis=1)
-    return( dfout )
+
+    if dfout.shape[0] > 0:
+        badnames = get_names_from_data_frame( ['Unnamed'], dfout )
+        dfout=dfout.drop(badnames, axis=1)
+    return dfout
 
 def enantiomorphic_filling_without_mask( image, axis=0, intensity='low' ):
     """

{antspymm-1.3.4.dist-info → antspymm-1.3.6.dist-info}/METADATA

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.4
+Version: 1.3.6
 Summary: multi-channel/time-series medical image processing with antspyx
-Home-page: https://github.com/stnava/ANTsPyMM
-Author: Avants, Gosselin, Tustison, Reardon
-Author-email: stnava@gmail.com
+Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: h5py >=2.10.0
 Requires-Dist: numpy >=1.19.4
 Requires-Dist: pandas >=1.0.1
 Requires-Dist: antspyx
-Requires-Dist: antspyt1w >=0.2.3
+Requires-Dist: antspynet >=0.2.5
+Requires-Dist: antspyt1w >=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -35,7 +35,7 @@ production environments.
 install the `dev` version by calling (within the source directory):
 
 ```
-python setup.py install
+python3 -m  build .
 ```
 
 or install the latest release via 
@@ -450,9 +450,12 @@ ssl._create_default_https_context = ssl._create_unverified_context
 
 ## to publish a release
 
+before doing this - make sure you have a recent run of `pip-compile pyproject.toml`
+
 ```
 rm -r -f build/ antspymm.egg-info/ dist/
-python3 setup.py sdist bdist_wheel
-twine upload --repository antspymm dist/*
+python3 -m  build .
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository antspymm dist/*
 ```
 

antspymm-1.3.6.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
+antspymm/mm.py,sha256=4g15BkmRyIn-ZTB7DOT9ggTDt-Ma3be44zKpCTALikY,479806
+antspymm-1.3.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.3.6.dist-info/METADATA,sha256=CRZs-L_1fv4rQPaKsMDPK0_9SHr6BLEyieHo30fLctw,14684
+antspymm-1.3.6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+antspymm-1.3.6.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.3.6.dist-info/RECORD,,

antspymm-1.3.4.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
-antspymm/mm.py,sha256=FbboL-Mdg6KTzWvAm770qaKEMLB9wK_isrBmqVbqyQw,478666
-antspymm-1.3.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.3.4.dist-info/METADATA,sha256=EwUjVut7HWbQQlz-kUaf5qFrfYXXuPXPL5mmeiXdW3A,14590
-antspymm-1.3.4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-antspymm-1.3.4.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.3.4.dist-info/RECORD,,