rapidtide 3.0a10__py3-none-any.whl → 3.0a11__py3-none-any.whl

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/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/__init__.py

@@ -1,4 +1,3 @@
 # -*- coding: utf-8 -*-
 from . import _version
-
-__version__ = _version.get_versions()["version"]
+__version__ = _version.get_versions()['version']

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

@@ -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/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/tests/test_fastresampler.py

@@ -16,12 +16,15 @@
 #   limitations under the License.
 #
 #
+import os
+
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
 from rapidtide.resample import FastResampler, FastResamplerFromFile
 from rapidtide.tests.utils import mse
+from rapidtide.tests.utils import get_test_temp_path
 
 
 def test_FastResampler(debug=False):
@@ -45,8 +48,9 @@ def test_FastResampler(debug=False):
         print(f"{genlaggedtc.hiresstart=}, {genlaggedtc.hiresend=}, {genlaggedtc.hiresstep=}")
 
     # save and reload with another name
-    genlaggedtc.save("savedresampler")
-    genlaggedtc2 = FastResamplerFromFile("savedresampler", padtime=padtime, debug=debug)
+    resamplername = os.path.join(get_test_temp_path(), "savedresampler")
+    genlaggedtc.save(resamplername)
+    genlaggedtc2 = FastResamplerFromFile(resamplername, padtime=padtime, debug=debug)
     if debug:
         print(f"{genlaggedtc2.initstart=}, {genlaggedtc2.initend=}, {genlaggedtc2.initstep=}")
         print(f"{genlaggedtc2.hiresstart=}, {genlaggedtc2.hiresend=}, {genlaggedtc2.hiresstep=}")

rapidtide/tests/test_fullrunhappy_v1.py

@@ -36,7 +36,6 @@ def test_fullrunhappy_v1(debug=False, displayplots=False):
         "--spatialglm",
         "--model",
         "model_revised",
-        "--aliasedcorrelation",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 

rapidtide/tests/test_fullrunhappy_v4.py

@@ -41,6 +41,7 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
         "model_revised",
         "--motionfile",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        "--aliasedcorrelation",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 

rapidtide/tests/test_runmisc.py

@@ -22,7 +22,7 @@ import matplotlib as mpl
 
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.showtc as showtc
-from rapidtide.tests.utils import get_examples_path
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
 def test_runmisc(debug=False, displayplots=False):
@@ -35,7 +35,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--sampletime",
         "12.5",
         "--tofile",
-        "showtcout1.jpg",
+        os.path.join(get_test_temp_path(), "showtcout1.jpg"),
         "--starttime",
         "100",
         "--endtime",
@@ -55,7 +55,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--displaytype",
         "power",
         "--tofile",
-        "showtcout2.jpg",
+        os.path.join(get_test_temp_path(), "showtcout2.jpg"),
         "--noxax",
         "--noyax",
         "--nolegend",
@@ -90,7 +90,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--displaytype",
         "phase",
         "--tofile",
-        "showtcout3.jpg",
+        os.path.join(get_test_temp_path(), "showtcout3.jpg"),
     ]
     pf.generic_init(showtc._get_parser, showtc.showtc, inputargs=inputargs)
 

rapidtide/workflows/tidepool.py

@@ -87,7 +87,7 @@ def _get_parser():
         "--dataset",
         nargs="*",
         help=(
-            "Use this dataset root name (skip initial selection step).  The root name is the entire path "
+            "Specify one or more dataset root names (skip initial selection step).  The root name is the entire path "
             "to the rapidtide output data (including the underscore) that precedes 'desc-maxtime_map.nii.gz'"
         ),
         dest="datafileroot",
@@ -106,8 +106,12 @@ def _get_parser():
         "--uistyle",
         action="store",
         type=str,
-        choices=["normal", "old", "big"],
-        help="Set the window layout style.  Default is 'normal'.",
+        choices=["normal", "big"],
+        help=(
+            "Set the window layout style.  The 'normal' uistyle loads 8 data maps into display panes, "
+            "and fits comfortably on the screen of a 14in MacbookPro screen.  The 'big' uistyle has 16 display "
+            "panes, and fits on a 16in MBP screen.  Default is 'normal'."
+        ),
         default="normal",
     )
     parser.add_argument(
@@ -120,7 +124,7 @@ def _get_parser():
     )
     parser.add_argument(
         "--ignoredimmatch",
-        help="Do not check to see if dataset sizes match",
+        help="Do not check to see if dataset sizes match.  This is almost certainly a terrible idea.",
         dest="ignoredimmatch",
         action="store_true",
         default=False,
@@ -1114,6 +1118,7 @@ def setMask(maskname):
         }
     print(maskinfodicts[maskname]["msg"])
     ui.setMask_Button.setText(maskinfodicts[maskname]["label"])
+    currentdataset.setFuncMaskName(maskname)
     for themap in currentdataset.loadedfuncmaps:
         if maskname == "nomask":
             overlays[themap].setFuncMask(None)
@@ -1149,16 +1154,19 @@ def overlay_radioButton_clicked(which, enabled):
                 thedispmin = overlays[currentdataset.focusmap].dispmin
                 thedispmax = overlays[currentdataset.focusmap].dispmax
             if verbosity > 1:
-                print("currentdataset.focusmap set to ", currentdataset.focusmap)
-            if overlays[currentdataset.focusmap].lut_state == gen_gray_state():
+                print(f"currentdataset.focusmap set to {currentdataset.focusmap}")
+                print(
+                    f"overlays[currentdataset.focusmap].LUTname set to {overlays[currentdataset.focusmap].LUTname}"
+                )
+            if overlays[currentdataset.focusmap].LUTname == "gray":
                 ui.gray_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_thermal_state():
+            elif overlays[currentdataset.focusmap].LUTname == "thermal":
                 ui.thermal_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_plasma_state():
+            elif overlays[currentdataset.focusmap].LUTname == "plasma":
                 ui.plasma_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_viridis_state():
+            elif overlays[currentdataset.focusmap].LUTname == "viridis":
                 ui.viridis_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_turbo_state():
+            elif overlays[currentdataset.focusmap].LUTname == "turbo":
                 ui.turbo_radioButton.setChecked(True)
             else:
                 ui.rainbow_radioButton.setChecked(True)
@@ -1563,9 +1571,10 @@ def activateDataset(currentdataset, ui, win, defaultdict, overlayGraphicsViews,
         overlays["atlas"].setGeomMask(thegeommask)
         overlays["atlas"].setFuncMask(overlays["atlasmask"].data)
 
-    if verbosity > 0:
-        for theoverlay in overlays:
-            overlays[theoverlay].summarize()
+    if not panesinitialized:
+        if verbosity > 0:
+            for theoverlay in overlays:
+                overlays[theoverlay].summarize()
 
     if verbosity > 1:
         print("focusmap is:", currentdataset.focusmap, "bgmap is:", bgmap)
@@ -1668,6 +1677,11 @@ def activateDataset(currentdataset, ui, win, defaultdict, overlayGraphicsViews,
         updateRegressor()
         updateRegressorSpectrum()
 
+        # update the mask menu
+        if currentdataset.funcmaskname is not None:
+            print(f"updating the mask menu to {currentdataset.funcmaskname}")
+            setMask(currentdataset.funcmaskname)
+
 
 def loadpane(
     themap,
@@ -2457,4 +2471,9 @@ def tidepool(args):
     updateRegressorSpectrum()
     uiinitialized = True
 
+    # for profiling
+    """for i in range(20):
+        selectDataset((i + 1) % 2)
+    sys.exit(0)"""
+
     QtWidgets.QApplication.instance().exec()

{rapidtide-3.0a10.dist-info → rapidtide-3.0a11.dist-info}/METADATA

@@ -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.dist-info → rapidtide-3.0a11.dist-info}/RECORD

@@ -6,11 +6,11 @@ cloud/mount-and-run,sha256=x6829t-u2vH1NpjxaaES39dv393E5EIv3S0WYdgLytY,2465
 cloud/rapidtide-HCPYA,sha256=e3GJeE2_O_x-eGqvPJ6qWp6g4T_askxrsM-PTpRdEjc,949
 cloud/rapidtide-cloud-test,sha256=SATOwGo4QYLvt-6hE0e3wyK9JjuDU5XzfLrfMoybvcY,466
 cloud/simple-cp-test,sha256=5ef8wmLfcKdny59BV6_DnAPj7O_mi0rOHdFZVN2iiLA,421
-rapidtide/Colortables.py,sha256=e3oktGI1OlC5NJSKzKiJG6dr_ONzm4uvyOo330IHh8w,4701
+rapidtide/Colortables.py,sha256=AQC-aHwgemxZNKtf8du7Oe08IKKxuOsUF1bDEdSyleY,5804
 rapidtide/OrthoImageItem.py,sha256=uN-fMX4vVB00-AFoUnfOXXq1qjLXruzOqYttNJYpIpM,21669
-rapidtide/RapidtideDataset.py,sha256=-URtXq-cpI5VaG7ae-8iiZZReeR7DBQ-O0jMxKysFW8,51622
-rapidtide/__init__.py,sha256=cECnPfGNIWXETiummGLjKcNXLROSDiFlLp-RpZSavwc,97
-rapidtide/_version.py,sha256=DOQAt5wVTS8zfWbgneAVv-s1QG9aCJHhnH8kpwzkmH8,24559
+rapidtide/RapidtideDataset.py,sha256=BEGznVDvLzL1Cd9TtuwicCYXcVug8hX1t-6qnEjMEDg,52239
+rapidtide/__init__.py,sha256=DrceP8tLrtTWV8PwS7YAgw6NuFkKAREFM7FsTaZob-s,96
+rapidtide/_version.py,sha256=cTDBv24D1_YgVeFU_x3GvlNlQD-clOji6E0Sb34osJY,24506
 rapidtide/calcandfitcorrpairs.py,sha256=UmCp9eSU--HCYd7frdO9ctnMeDK32D1Eb53b1hdzw9w,7397
 rapidtide/calccoherence.py,sha256=SjSWcqbyATKu5Hya5LgRCTfq2w9l7G9L_kZbol802sk,4512
 rapidtide/calcnullsimfunc.py,sha256=_L5Gxr1CI0GKmGmEjHzrYNufAzDchDsruYCzboSgw3s,7150
@@ -62,12 +62,12 @@ rapidtide/data/examples/src/testcomplex,sha256=PFY_d30eqYBx5K8cPP_WxsP2YPlYuawo8
 rapidtide/data/examples/src/testdecomp,sha256=xxxr510aOBjtpJy4aQNAFTyEFZD6QdHp6-Aa_esYalY,269
 rapidtide/data/examples/src/testfileorfloat,sha256=9r4mz7pBV_8iFZya9kmtfbnTRS3-94Cx9Q63Ni3mkZs,815
 rapidtide/data/examples/src/testfingerprint,sha256=RlAIC1lMDWMGzZKxY24DJRuaUEL0BenSFBey0gL5dqU,402
-rapidtide/data/examples/src/testfmri,sha256=BIrd4dFeOgu3s1DZt-msEiSk9C2hTvcPFhSV57wBlyg,3012
+rapidtide/data/examples/src/testfmri,sha256=vLftCOpC0rWy0QNNv-7FdWvDQLBRPOYIEYlViXn2r8g,3161
 rapidtide/data/examples/src/testfmridocker,sha256=jjL7bK29rrcog6uO9BtvcyAU3Sv8_5cbw2nqKoiZ95o,1193
 rapidtide/data/examples/src/testfrozen,sha256=K3qUWDRKPPiCXRgIFuPdwUUjUTzf4QBW8UUhR75NzDM,283
 rapidtide/data/examples/src/testfuncs,sha256=QmVJP8vjr-HqKCAaIz7McdADVZru6Nvwq16h5KPs9ek,1551
 rapidtide/data/examples/src/testglmfilt,sha256=LD2cTB-7yyCc31jAr8UtYksf-Cn-YLC3ScnV3olvpFE,3333
-rapidtide/data/examples/src/testhappy,sha256=Qo-hNofuIYOj522PPtqR_5pePTTTyJTaOdAA18G3bkg,1817
+rapidtide/data/examples/src/testhappy,sha256=7dKe3PM-nPRbsroGRq3RQFFABPdNuByS3aEddgu_Oyc,1712
 rapidtide/data/examples/src/testlinfit,sha256=oPnkHJ6lcwsuJhnSMMK7Gx3DHSCf6JK7CIYuIMHbyNA,471
 rapidtide/data/examples/src/testlocalflow,sha256=hEwstisbWVuALr_29fBJ2nHETKkEF_9qK8wJ4kzuiJk,596
 rapidtide/data/examples/src/testnoiseamp,sha256=ZRu3GstBhdnwZmDF7ExZynOXFFMElWiZuod8LbUKa-I,612
@@ -212,13 +212,13 @@ rapidtide/tests/test_correlate.py,sha256=GIbG5btp-dJS-cOyMrxPcweOWIa--zWVNSfrfnl
 rapidtide/tests/test_corrpass.py,sha256=eBNw1KBvjo9WgorR-7aPga3WIeQxckTGjPwv-kn6zBw,7836
 rapidtide/tests/test_delayestimation.py,sha256=2AeQcT_cFvvNvH0R-K9WNDDp66S-UjybfAqdfG0REYU,13460
 rapidtide/tests/test_doresample.py,sha256=ILQxH6UXtHZ9OwgTpbZE_bek_QKYGmmA6D70r6NqAoc,2716
-rapidtide/tests/test_fastresampler.py,sha256=UOWk2_GXEp0xT_gOkVnvg7yuQbbkZGHdljB6zh28OJQ,3763
+rapidtide/tests/test_fastresampler.py,sha256=OIQFWJhSlENB2uoJdIEqYg5O1rzhBDxAbRuw-nyMOL0,3894
 rapidtide/tests/test_filter.py,sha256=_xhk3rbYFtuKgrDdgrrrlITtmQhOUUi5EhFcnxVUioA,10891
 rapidtide/tests/test_findmaxlag.py,sha256=x9mKQ8TmWW4jq8CrlfrX8zwO3n4pYa7aPgF3F1e0aPc,11551
-rapidtide/tests/test_fullrunhappy_v1.py,sha256=XuK90R4Ef7PIvJfyyXHqL__SvRjJUHtHX8PZYuJjEKo,1502
+rapidtide/tests/test_fullrunhappy_v1.py,sha256=axS-rLLHUKT-VN-Vv2OVlGGra9x879X_twOAdgeCuhE,1470
 rapidtide/tests/test_fullrunhappy_v2.py,sha256=9_1sjtTP-4YVv-d86iL0hkm8T8ODQ1Ckumu-iFu2W8s,1935
 rapidtide/tests/test_fullrunhappy_v3.py,sha256=sEWV-Qf_13gJ9BnUmgIu-JtMAh1Jp0Qn8EhTEBU4YmU,1743
-rapidtide/tests/test_fullrunhappy_v4.py,sha256=_8ax0oEEdaSSRa-N-lGquWP4MfLj6DR-xy-NUZ3kuhM,1721
+rapidtide/tests/test_fullrunhappy_v4.py,sha256=YL6FWWAL2eeNg-EdaOhdq6r4-84lF_f36hQoGYBl0f4,1753
 rapidtide/tests/test_fullrunhappy_v5.py,sha256=1otOjGN7PADurvB3PUqHq_FxCpd5vr3Q1KD8FrPGXlU,1721
 rapidtide/tests/test_fullrunrapidtide_v1.py,sha256=jO2PyPTvxfIYyzydQgxD812DRuzotCTFmnBqShRpa0M,2864
 rapidtide/tests/test_fullrunrapidtide_v2.py,sha256=RsMCrq-A4WzVzQxFnyvuotKCT4ipfyepM1RxGBpmMys,2881
@@ -236,7 +236,7 @@ rapidtide/tests/test_padvec.py,sha256=UKALfQyS9v87QiThxSu51Md3eXkChTpTfm-C0KdXcR
 rapidtide/tests/test_phaseanalysis.py,sha256=DMzB19c9rz3c5PSwXO4QYOEqNLR85YZLra4wV33O6uI,2150
 rapidtide/tests/test_rapidtideparser.py,sha256=HBoZdmS5UEGDFvlpueNhYXvVbq-pWrhNDCofkc2Tp98,5555
 rapidtide/tests/test_refinedelay.py,sha256=HMM8nb65LYLF8AIgnVTtNUVtf6lt4sc66q9T60WqflY,8460
-rapidtide/tests/test_runmisc.py,sha256=xeeE5AZc2naWfgX9izoLIwXTnU2kpD6QbRxzih61JFc,2727
+rapidtide/tests/test_runmisc.py,sha256=rrhn_kAnid2c26WgCGr3Va3SfPo14m_bN2p9MOafUH8,2855
 rapidtide/tests/test_sharedmem.py,sha256=Yp5WuYMdKABfqYKvuayq5253pvOC05V_oUK-povjGV8,2026
 rapidtide/tests/test_simulate.py,sha256=m8oGp8qrxQv-FtxX6P3t_nu8bvSizWSZXIij5rtWB6k,3325
 rapidtide/tests/test_stcorrelate.py,sha256=jfg1t-tyfrU5ZmlFP9fjAfysnqJ2BTUFOI6cVBt8qHA,2493
@@ -325,12 +325,12 @@ rapidtide/workflows/spectrogram.py,sha256=ATe6baNL-Rv6rvV6rCcxcBO2naFu0v4UDJ2hX6
 rapidtide/workflows/synthASL.py,sha256=fRfu2lAQwC1Ahi_Sz-mvmp3yZCV_zUWFbu8F9-8RHxM,4971
 rapidtide/workflows/tcfrom2col.py,sha256=El9pjrCfxANFA3s60YvHOTUx3UYaavJgCOIYtMcvKlk,1936
 rapidtide/workflows/tcfrom3col.py,sha256=6tV2lGEtXpI4dn_8kcTCVzZxpJzmopuDwpXvOIE7vzQ,1938
-rapidtide/workflows/tidepool.py,sha256=8vM8fXmw9Zew-vUZRGjRPcNmCTxaH6YHINgb4JWemlA,85603
+rapidtide/workflows/tidepool.py,sha256=14yrUQ87syFeTuU0lJBxVz3rBrwV9f4A4fGwVW5Bj_g,86399
 rapidtide/workflows/utils.py,sha256=k2m2F1-tWxhcUYvk5geO1yl-c5bKcDX7Jv7ohvJZaOk,5379
 rapidtide/workflows/variabilityizer.py,sha256=yQFDTBcGehxW44R_FQHeeKrTpeYrrh96xcW1uWbPtYo,3167
-rapidtide-3.0a10.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-rapidtide-3.0a10.dist-info/METADATA,sha256=Jc1StyHH9MUs_GE6aj6wi3L1xnuMmwQSD61o4VQTNEA,15624
-rapidtide-3.0a10.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-rapidtide-3.0a10.dist-info/entry_points.txt,sha256=76O4RdCVLd7YrASvmgJQWaRUlgmBzMDU5_XkGIlmuTk,3260
-rapidtide-3.0a10.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
-rapidtide-3.0a10.dist-info/RECORD,,
+rapidtide-3.0a11.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+rapidtide-3.0a11.dist-info/METADATA,sha256=zVdYRWhcyzi1lh3_CiHvi_yduUOXQLzLep58HsqEQuA,15624
+rapidtide-3.0a11.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+rapidtide-3.0a11.dist-info/entry_points.txt,sha256=76O4RdCVLd7YrASvmgJQWaRUlgmBzMDU5_XkGIlmuTk,3260
+rapidtide-3.0a11.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
+rapidtide-3.0a11.dist-info/RECORD,,