rapidtide 3.0a10__py3-none-any.whl → 3.0a12__py3-none-any.whl

rapidtide/_version.py

@@ -1,3 +1,4 @@
+
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -11,12 +12,12 @@
 """Git implementation of _version.py."""
 
 import errno
-import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
+import functools
 
 
 def get_keywords() -> Dict[str, str]:
@@ -67,14 +68,12 @@ HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
     """Create decorator to mark a method as the handler of a VCS."""
-
     def decorate(f: Callable) -> Callable:
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
-
     return decorate
 
 
@@ -101,14 +100,10 @@ def run_command(
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            process = subprocess.Popen(
-                [command] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-                **popen_kwargs,
-            )
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None), **popen_kwargs)
             break
         except OSError as e:
             if e.errno == errno.ENOENT:
@@ -146,21 +141,15 @@ def versions_from_parentdir(
     for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {
-                "version": dirname[len(parentdir_prefix) :],
-                "full-revisionid": None,
-                "dirty": False,
-                "error": None,
-                "date": None,
-            }
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
         rootdirs.append(root)
         root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
-        )
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -223,7 +212,7 @@ def git_versions_from_keywords(
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)}
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -232,7 +221,7 @@ def git_versions_from_keywords(
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = {r for r in refs if re.search(r"\d", r)}
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -240,36 +229,32 @@ def git_versions_from_keywords(
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
             # Filter out refs that exactly match prefix or that don't start
             # with a number once the prefix is stripped (mostly a concern
             # when prefix is '')
-            if not re.match(r"\d", r):
+            if not re.match(r'\d', r):
                 continue
             if verbose:
                 print("picking %s" % r)
-            return {
-                "version": r,
-                "full-revisionid": keywords["full"].strip(),
-                "dirty": False,
-                "error": None,
-                "date": date,
-            }
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {
-        "version": "0+unknown",
-        "full-revisionid": keywords["full"].strip(),
-        "dirty": False,
-        "error": "no suitable tags",
-        "date": None,
-    }
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
 def git_pieces_from_vcs(
-    tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command
+    tag_prefix: str,
+    root: str,
+    verbose: bool,
+    runner: Callable = run_command
 ) -> Dict[str, Any]:
     """Get version from 'git describe' in the root of the source tree.
 
@@ -288,7 +273,8 @@ def git_pieces_from_vcs(
     env.pop("GIT_DIR", None)
     runner = functools.partial(runner, env=env)
 
-    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose)
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=not verbose)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -296,19 +282,10 @@ def git_pieces_from_vcs(
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = runner(
-        GITS,
-        [
-            "describe",
-            "--tags",
-            "--dirty",
-            "--always",
-            "--long",
-            "--match",
-            f"{tag_prefix}[[:digit:]]*",
-        ],
-        cwd=root,
-    )
+    describe_out, rc = runner(GITS, [
+        "describe", "--tags", "--dirty", "--always", "--long",
+        "--match", f"{tag_prefix}[[:digit:]]*"
+    ], cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -323,7 +300,8 @@ def git_pieces_from_vcs(
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
-    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root)
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
     # --abbrev-ref was added in git-1.6.3
     if rc != 0 or branch_name is None:
         raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
@@ -363,16 +341,17 @@ def git_pieces_from_vcs(
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[: git_describe.rindex("-dirty")]
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
             return pieces
 
         # tag
@@ -381,9 +360,10 @@ def git_pieces_from_vcs(
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix)
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -432,7 +412,8 @@ def render_pep440(pieces: Dict[str, Any]) -> str:
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -461,7 +442,8 @@ def render_pep440_branch(pieces: Dict[str, Any]) -> str:
         rendered = "0"
         if pieces["branch"] != "master":
             rendered += ".dev0"
-        rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -622,13 +604,11 @@ def render_git_describe_long(pieces: Dict[str, Any]) -> str:
 def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {
-            "version": "unknown",
-            "full-revisionid": pieces.get("long"),
-            "dirty": None,
-            "error": pieces["error"],
-            "date": None,
-        }
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -652,13 +632,9 @@ def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
 
 
 def get_versions() -> Dict[str, Any]:
@@ -672,7 +648,8 @@ def get_versions() -> Dict[str, Any]:
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
     except NotThisMethod:
         pass
 
@@ -681,16 +658,13 @@ def get_versions() -> Dict[str, Any]:
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for _ in cfg.versionfile_source.split("/"):
+        for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
-        return {
-            "version": "0+unknown",
-            "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to find root of source tree",
-            "date": None,
-        }
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -704,10 +678,6 @@ def get_versions() -> Dict[str, Any]:
     except NotThisMethod:
         pass
 
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}

rapidtide/data/examples/src/testfmri

@@ -1,126 +1,10 @@
 #!/bin/bash
 
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --glmderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_norefine
-
-rapidtide \
-    --spatialfilt 5 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    --refinedelay \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_filt
-
 rapidtide \
-    --spatialfilt 0 \
+    --spatialfilt -1 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --refinedelay \
+    --outputlevel max \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nofilt
-
-#rapidtide \
-#    --spatialfilt 5 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --refinedelay \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_corr
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 50 \
-#    --despecklepasses 50 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_spec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --passes 4 \
-#    --despecklepasses 5 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingspec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingnospec
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--padtype constant \
-    #--outputlevel max \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_constantpad
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --simcalcrange 50 -1 \
-#    --memprofile \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_memprofile
-
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_excludemask
-#
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--tincludemask tmask3.txt \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_bothmasks
-
-#for FILT in 1 2 4 8 16
-#do
-#    rapidtide \
-#        --spatialfilt ${FILT} \
-#        --nprocs -1 \
-#        --passes 3 \
-#        --simcalcrange 50 -1 \
-#        --outputlevel min \
-#        sub-RAPIDTIDETEST.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_${FILT}
-#done
-#
-#for MAP in maxtime maxcorr
-#do
-#    fslmerge -t ../dst/all_${MAP} \
-#        ../dst/sub-RAPIDTIDETEST_1_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_2_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_4_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_8_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_16_desc-${MAP}_map.nii.gz 
-#done
+    ../dst/sub-RAPIDTIDETEST

rapidtide/data/examples/src/testhappy

@@ -65,10 +65,5 @@
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
+    --spatialglm \
     ../dst/happy
-
-happy \
-    sub-HAPPYTEST.nii.gz \
-    sub-HAPPYTEST.json \
-    ../dst/happy_aliasedcorrelation \
-    --aliasedcorrelation

rapidtide/data/examples/src/testinitdelay

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_defaultfilt
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --regressor ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-movingregressor_timeseries.json:pass3 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-maxtimerefined_map.nii.gz \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_startfromlast

rapidtide/data/examples/src/testnewrefine

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineglmderivs 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineglmderivs 2 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv
+
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to1 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 1 \
+    --outputlevel max
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv \
+    --alternateoutput ../dst/retrotest_2to1 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 1 \
+    --outputlevel max
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to2 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 2 \
+    --outputlevel max

rapidtide/data/examples/src/testrefineonly

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --passes 1 \
+    --nodelayfit \
+    --focaldebug \
+    --dofinalrefine \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_firstpass
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --nodelayfit \
+    --regressor ../dst/sub-RAPIDTIDETEST_firstpass_desc-refinedmovingregressor_timeseries.json:filtered_pass1 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_firstpass_desc-maxtimerefined_map.nii.gz \
+    --dofinalrefine \
+    --passes 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_secondpass

rapidtide/glmpass.py

@@ -17,6 +17,7 @@
 #
 #
 import numpy as np
+from scipy.special import factorial
 from tqdm import tqdm
 
 import rapidtide.filter as tide_filt
@@ -350,11 +351,17 @@ def makevoxelspecificderivs(theevs, nderivs=1, debug=False):
     if nderivs == 0:
         thenewevs = theevs
     else:
+        taylorcoffs = np.zeros((nderivs + 1), dtype=np.float64)
+        taylorcoffs[0] = 1.0
         thenewevs = np.zeros((theevs.shape[0], theevs.shape[1], nderivs + 1), dtype=float)
+        for i in range(1, nderivs + 1):
+            taylorcoffs[i] = 1.0 / factorial(i)
         for thevoxel in range(0, theevs.shape[0]):
             thenewevs[thevoxel, :, 0] = theevs[thevoxel, :] * 1.0
             for i in range(1, nderivs + 1):
-                thenewevs[thevoxel, :, i] = np.gradient(thenewevs[thevoxel, :, i - 1])
+                thenewevs[thevoxel, :, i] = taylorcoffs[i] * np.gradient(
+                    thenewevs[thevoxel, :, i - 1]
+                )
     if debug:
         print(f"{nderivs=}")
         print(f"{thenewevs.shape=}")