rapidtide 3.0a10__tar.gz → 3.0a11__tar.gz

{rapidtide-3.0a10 → rapidtide-3.0a11}/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Release history
 
+## Version 3.0alpha11 (3/5/25)
+* (tidepool) Substantial speed improvement switching datasets.
+* (tidepool) Colormap radio button is now set correctly.
+* (tidepool) Mask menu label is now set correctly when restoring a loaded dataset.
+* (versioneer) Updated to 0.29.
+* (docs) Tidepool's new functionality is now described.
+
 ## Version 3.0alpha10 (2/28/25)
 * (tidepool) Full support for multiple concurrent datasets.  Dataset loading and selection is now done through the File menu.
 * (tidepool) Load additional informational maps, and somewhat more intelligently.

{rapidtide-3.0a10/rapidtide.egg-info → rapidtide-3.0a11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a10
+Version: 3.0a11
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>

{rapidtide-3.0a10 → rapidtide-3.0a11}/TODO.md

@@ -2,9 +2,10 @@ To do list
 ----------
 
 1. (package) Expand automated testing
-4. (tidepool) Implement ASPECTS averaging
+4. (tidepool) Implement ASPECTS/JHU averaging
 7. (rapidtide) Implement a dispersive delay model
 8. (rapidtide) Add a sinc peak fit
+9. (tidepool) Fix the weird limit resetting bug when some panes are activated.
 
 Implement new argument parsing:
 rapidtide/experimental/highresmotion

{rapidtide-3.0a10 → rapidtide-3.0a11}/pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ['setuptools>=42', 'cffi>=1.0.0', 'versioneer[toml]']
-build-backend = 'setuptools.build_meta'
+requires = ['setuptools>=42', 'cffi>=1.0.0', 'versioneer[toml]==0.29']
+build-backend = "setuptools.build_meta"
 
 [project]
 name = 'rapidtide'
@@ -41,8 +41,7 @@ dependencies = [
   'tqdm',
   'versioneer',
 ]
-#dynamic = ['version', 'license', 'keywords']
-dynamic = ['version']
+dynamic = ["version"]
 authors = [
     {name = 'Blaise deB. Frederick', email='blaise.frederick@gmail.com'},
     {name = 'Taylor Salo'},

{rapidtide-3.0a10 → rapidtide-3.0a11}/rapidtide/Colortables.py

@@ -63,37 +63,55 @@ def setendalpha(thestate, alpha, debug=False):
 def gen_thermal_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["thermal"]
+    thegradient = Gradients["thermal"]
+    thegradient["name"] = "thermal"
+    return thegradient
+    #return Gradients["thermal"]
 
 
 def gen_flame_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["flame"]
+    thegradient = Gradients["flame"]
+    thegradient["name"] = "flame"
+    return thegradient
+    #return Gradients["flame"]
 
 
 def gen_yellowy_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["yellowy"]
+    thegradient = Gradients["yellowy"]
+    thegradient["name"] = "yellowy"
+    return thegradient
+    #return Gradients["yellowy"]
 
 
 def gen_bipolar_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["bipolar"]
+    thegradient = Gradients["bipolar"]
+    thegradient["name"] = "bipolar"
+    return thegradient
+    #return Gradients["bipolar"]
 
 
 def gen_spectrum_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["spectrum"]
+    thegradient = Gradients["spectrum"]
+    thegradient["name"] = "spectrum"
+    return thegradient
+    #return Gradients["spectrum"]
 
 
 def gen_turbo_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["turbo"]
+    thegradient = Gradients["turbo"]
+    thegradient["name"] = "turbo"
+    return thegradient
+    #return Gradients["turbo"]
 
 
 def gen_gray_state():
@@ -103,6 +121,7 @@ def gen_gray_state():
             (1.0000, (255, 255, 255, 255)),
         ],
         "mode": "rgb",
+        "name": "gray",
     }
 
 
@@ -113,31 +132,44 @@ def gen_grey_state():
             (1.0000, (255, 255, 255, 255)),
         ],
         "mode": "rgb",
+        "name": "grey",
     }
 
 
 def gen_viridis_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["viridis"]
+    thegradient = Gradients["viridis"]
+    thegradient["name"] = "viridis"
+    return thegradient
+    #return Gradients["viridis"]
 
 
 def gen_inferno_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["inferno"]
+    thegradient = Gradients["inferno"]
+    thegradient["name"] = "inferno"
+    return thegradient
+    #return Gradients["inferno"]
 
 
 def gen_plasma_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["plasma"]
+    thegradient = Gradients["plasma"]
+    thegradient["name"] = "plasma"
+    return thegradient
+    #return Gradients["plasma"]
 
 
 def gen_magma_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["magma"]
+    thegradient = Gradients["magma"]
+    thegradient["name"] = "magma"
+    return thegradient
+    #return Gradients["magma"]
 
 
 def gen_g2y2r_state():
@@ -150,6 +182,7 @@ def gen_g2y2r_state():
             (1.0000, (255, 0, 0, 0)),
         ],
         "mode": "rgb",
+        "name": "g2y2r",
     }
 
 
@@ -157,6 +190,7 @@ def gen_mask_state():
     return {
         "ticks": [(0.0000, (0, 0, 0, 255)), (1.0000, (255, 255, 255, 0))],
         "mode": "rgb",
+        "name": "mask",
     }
 
 
@@ -168,6 +202,7 @@ def gen_greyclip_state():
             (1.0, (255, 0, 0, 255)),
         ],
         "mode": "rgb",
+        "name": "greyclip",
     }
 
 

{rapidtide-3.0a10 → rapidtide-3.0a11}/rapidtide/RapidtideDataset.py

@@ -161,6 +161,7 @@ class Timecourse:
 
 class Overlay:
     "Store a data overlay and some information about it"
+    LUTname = None
 
     def __init__(
         self,
@@ -193,6 +194,7 @@ class Overlay:
         self.namebase = namebase
         if self.verbose > 1:
             print("reading map ", self.name, " from ", self.filename, "...")
+        self.maskhash = 0
         self.invertonload = invertonload
         self.readImageData(isaMask=isaMask)
         self.mask = None
@@ -277,6 +279,7 @@ class Overlay:
 
     def updateStats(self):
         calcmaskeddata = self.data[np.where(self.mask != 0)]
+
         self.minval = calcmaskeddata.min()
         self.maxval = calcmaskeddata.max()
         (
@@ -290,6 +293,7 @@ class Overlay:
             calcmaskeddata, bins=np.linspace(self.minval, self.maxval, 200)
         )
         self.quartiles = [self.pct25, self.pct50, self.pct75]
+
         if self.verbose > 1:
             print(
                 self.name,
@@ -402,9 +406,17 @@ class Overlay:
 
     def maskData(self):
         self.mask = self.geommask * self.funcmask
-        self.maskeddata = self.data.copy()
-        self.maskeddata[np.where(self.mask < 0.5)] = 0.0
-        self.updateStats()
+        maskhash = hash(self.mask.tostring())
+        # these operations are expensive, so only do them if the mask is changed
+        if (maskhash == self.maskhash) and (self.verbose > 1):
+            print("mask has not changed")
+        else:
+            if self.verbose > 1:
+                print("mask changed - recalculating")
+            self.maskeddata = self.data.copy()
+            self.maskeddata[np.where(self.mask < 0.5)] = 0.0
+            self.updateStats()
+            self.maskhash = maskhash
 
     def setReport(self, report):
         self.report = report
@@ -433,6 +445,7 @@ class Overlay:
             self.lut_state = setendalpha(lut_state, endalpha)
         self.gradient.restoreState(self.lut_state)
         self.theLUT = self.gradient.getLookupTable(512, alpha=True)
+        self.LUTname = lut_state["name"]
 
     def setisdisplayed(self, display_state):
         self.display_state = display_state
@@ -505,6 +518,7 @@ class RapidtideDataset:
         fileroot,
         anatname=None,
         geommaskname=None,
+        funcmaskname=None,
         graymaskspec=None,
         whitemaskspec=None,
         userise=False,
@@ -523,6 +537,7 @@ class RapidtideDataset:
         self.fileroot = fileroot
         self.anatname = anatname
         self.geommaskname = geommaskname
+        self.funcmaskname = funcmaskname
         self.graymaskspec = graymaskspec
         self.whitemaskspec = whitemaskspec
         self.userise = userise
@@ -1355,3 +1370,6 @@ class RapidtideDataset:
             self.focusmap = whichmap
         except KeyError:
             self.focusmap = "lagtimes"
+
+    def setFuncMaskName(self, maskname):
+        self.funcmaskname = maskname

rapidtide-3.0a11/rapidtide/__init__.py

@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+from . import _version
+__version__ = _version.get_versions()['version']

{rapidtide-3.0a10 → rapidtide-3.0a11}/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-3.0a10 → rapidtide-3.0a11}/rapidtide/data/examples/src/testfmri

@@ -9,23 +9,29 @@
 #    sub-RAPIDTIDETEST.nii.gz \
 #    ../dst/sub-RAPIDTIDETEST_norefine
 
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_defaultfilt
+
 rapidtide \
     --spatialfilt 5 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_filt
+    ../dst/sub-RAPIDTIDETEST_5mmfilt
 
 rapidtide \
     --spatialfilt 0 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nofilt
+    ../dst/sub-RAPIDTIDETEST_nospatialfilt
 
 #rapidtide \
 #    --spatialfilt 5 \

{rapidtide-3.0a10 → rapidtide-3.0a11}/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