rapidtide 3.0a13__py3-none-any.whl → 3.0a15__py3-none-any.whl

rapidtide/externaltools.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/fMRIData_class.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/filter.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -44,13 +44,6 @@ if pyfftwpresent:
     pyfftw.interfaces.cache.enable()
 
 # ----------------------------------------- Conditional imports ---------------------------------------
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
 try:
     from numba import jit
 except ImportError:

rapidtide/fit.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -40,13 +40,6 @@ MAXLINES = 10000000
 donotbeaggressive = True
 
 # ----------------------------------------- Conditional imports ---------------------------------------
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
 try:
     from numba import jit
 except ImportError:

rapidtide/happy_supportfuncs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2018-2024 Blaise Frederick
+#   Copyright 2018-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -535,6 +535,29 @@ def approximateentropy(waveform, m, r):
     return abs(_phi(m + 1) - _phi(m))
 
 
+def summarizerun(theinfodict, getkeys=False):
+    keylist = [
+        "corrcoeff_raw2pleth",
+        "corrcoeff_filt2pleth",
+        "E_sqi_mean_pleth",
+        "E_sqi_mean_bold",
+        "S_sqi_mean_pleth",
+        "S_sqi_mean_bold",
+        "K_sqi_mean_pleth",
+        "K_sqi_mean_bold",
+    ]
+    if getkeys:
+        return ",".join(keylist)
+    else:
+        outputline = []
+        for thekey in keylist:
+            try:
+                outputline.append(str(theinfodict[thekey]))
+            except KeyError:
+                outputline.append("")
+        return ",".join(outputline)
+
+
 def entropy(waveform):
     return -np.sum(np.square(waveform) * np.nan_to_num(np.log2(np.square(waveform))))
 
@@ -632,17 +655,23 @@ def calcplethquality(
         E_waveform[i] = approximateentropy(dt_waveform[startpt : endpt + 1], 2, r)
 
     S_sqi_mean = np.mean(S_waveform)
+    S_sqi_median = np.median(S_waveform)
     S_sqi_std = np.std(S_waveform)
     K_sqi_mean = np.mean(K_waveform)
+    K_sqi_median = np.median(K_waveform)
     K_sqi_std = np.std(K_waveform)
     E_sqi_mean = np.mean(E_waveform)
+    E_sqi_median = np.median(E_waveform)
     E_sqi_std = np.std(E_waveform)
 
     infodict["S_sqi_mean" + suffix] = S_sqi_mean
+    infodict["S_sqi_median" + suffix] = S_sqi_median
     infodict["S_sqi_std" + suffix] = S_sqi_std
     infodict["K_sqi_mean" + suffix] = K_sqi_mean
+    infodict["K_sqi_median" + suffix] = K_sqi_median
     infodict["K_sqi_std" + suffix] = K_sqi_std
     infodict["E_sqi_mean" + suffix] = E_sqi_mean
+    infodict["E_sqi_median" + suffix] = E_sqi_median
     infodict["E_sqi_std" + suffix] = E_sqi_std
 
     if outputlevel > 1:

rapidtide/helper_classes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/io.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/linfitfiltpass.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -97,6 +97,7 @@ def linfitfiltpass(
     mp_chunksize=1000,
     rt_floatset=np.float64,
     rt_floattype="float64",
+    verbose=True,
     debug=False,
 ):
     inputshape = np.shape(fmri_data)
@@ -184,6 +185,7 @@ def linfitfiltpass(
             GLM_consumer,
             inputshape,
             themask,
+            verbose=verbose,
             nprocs=nprocs,
             procbyvoxel=procbyvoxel,
             showprogressbar=showprogressbar,

rapidtide/makelaggedtcs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -24,8 +24,6 @@ from tqdm import tqdm
 
 import rapidtide.multiproc as tide_multiproc
 
-LGR = logging.getLogger("GENERAL")
-
 
 def _procOneVoxelMakelagtc(
     vox,
@@ -51,6 +49,7 @@ def makelaggedtcs(
     lagmask,
     lagtimes,
     lagtc,
+    LGR=None,
     nprocs=1,
     alwaysmultiproc=False,
     showprogressbar=True,
@@ -90,6 +89,7 @@ def makelaggedtcs(
             makelagtc_consumer,
             inputshape,
             lagmask,
+            verbose=(LGR is not None),
             nprocs=nprocs,
             showprogressbar=showprogressbar,
             chunksize=chunksize,
@@ -127,13 +127,16 @@ def makelaggedtcs(
                 )
                 volumetotal += 1
 
-    LGR.info(f"\nLagged timecourses created for {volumetotal} voxels")
+    if LGR is not None:
+        LGR.info(f"\nLagged timecourses created for {volumetotal} voxels")
 
     # garbage collect
     uncollected = gc.collect()
     if uncollected != 0:
-        LGR.info(f"garbage collected - unable to collect {uncollected} objects")
+        if LGR is not None:
+            LGR.info(f"garbage collected - unable to collect {uncollected} objects")
     else:
-        LGR.info("garbage collected")
+        if LGR is not None:
+            LGR.info("garbage collected")
 
     return volumetotal

rapidtide/maskutil.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/miscmath.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -47,13 +47,6 @@ MAXLINES = 10000000
 donotbeaggressive = True
 
 # ----------------------------------------- Conditional imports ---------------------------------------
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
 try:
     from numba import jit
 except ImportError:

rapidtide/multiproc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -77,8 +77,8 @@ def _process_data(data_in, inQ, outQ, showprogressbar=True, reportstep=1000, chu
                 pbar.update(1)
                 if numreturned > remainder - 1:
                     break
-
-    print()
+    if showprogressbar:
+        print()
 
     return data_out
 
@@ -88,6 +88,7 @@ def run_multiproc(
     inputshape,
     maskarray,
     nprocs=1,
+    verbose=True,
     procbyvoxel=True,
     showprogressbar=True,
     chunksize=1000,
@@ -105,13 +106,6 @@ def run_multiproc(
         workers = [ctx.Process(target=consumerfunc, args=(inQ, outQ)) for i in range(n_workers)]
         # signal.signal(signal.SIGINT, original_sigint_handler)
     else:
-        """# try adding this magic incantation to get coverage to record multiprocessing properly
-        # This fails for python 3.8 and above
-        try:
-            from pytest_cov.embed import cleanup
-        except ImportError:
-            cleanup = None
-        """
         cleanup = None  # just disable this for now
         inQ = mp.Queue()
         outQ = mp.Queue()
@@ -141,7 +135,8 @@ def run_multiproc(
             data_in.append(d)
         elif maskarray[d] > 0.5:
             data_in.append(d)
-    print("processing", len(data_in), procunit + " with", n_workers, "processes")
+    if verbose:
+        print("processing", len(data_in), procunit + " with", n_workers, "processes")
     data_out = _process_data(
         data_in, inQ, outQ, showprogressbar=showprogressbar, chunksize=chunksize
     )
@@ -162,6 +157,7 @@ def run_multithread(
     consumerfunc,
     inputshape,
     maskarray,
+    verbose=True,
     nprocs=1,
     procbyvoxel=True,
     showprogressbar=True,
@@ -197,7 +193,8 @@ def run_multithread(
             data_in.append(d)
         elif maskarray[d] > 0:
             data_in.append(d)
-    print("processing", len(data_in), procunit + " with", n_workers, "threads")
+    if verbose:
+        print("processing", len(data_in), procunit + " with", n_workers, "threads")
     data_out = _process_data(
         data_in, inQ, outQ, showprogressbar=showprogressbar, chunksize=chunksize
     )

rapidtide/patchmatch.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick (except for some routines listed below)
+#   Copyright 2016-2025 Blaise Frederick (except for some routines listed below)
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/peakeval.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

rapidtide/qualitycheck.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2024-2024 Blaise Frederick
+#   Copyright 2024-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.