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

rapidtide/refinedelay.py

@@ -17,6 +17,7 @@
 #
 #
 import numpy as np
+import numpy.polynomial.polynomial as poly
 from scipy.interpolate import CubicSpline, UnivariateSpline
 from scipy.ndimage import median_filter
 from statsmodels.robust import mad
@@ -25,7 +26,6 @@ import rapidtide.filter as tide_filt
 import rapidtide.io as tide_io
 import rapidtide.workflows.glmfrommaps as tide_glmfrommaps
 
-
 global ratiotooffsetfunc, maplimits
 
 
@@ -45,6 +45,7 @@ def trainratiotooffset(
     numpoints=501,
     smoothpts=3,
     edgepad=5,
+    glmderivs=1,
     debug=False,
 ):
     global ratiotooffsetfunc, maplimits
@@ -58,6 +59,7 @@ def trainratiotooffset(
         print("\tmaxdelay:", maxdelay)
         print("\tsmoothpts:", smoothpts)
         print("\tedgepad:", edgepad)
+        print("\tglmderivs:", glmderivs)
         print("\tlagtcgenerator:", lagtcgenerator)
     # make a delay map
     delaystep = (maxdelay - mindelay) / (numpoints - 1)
@@ -129,18 +131,32 @@ def trainratiotooffset(
         None,
         None,
         optiondict,
+        glmderivs=glmderivs,
         debug=debug,
     )
     if debug:
         print("before trimming")
         print(f"{glmderivratios.shape=}")
         print(f"{lagtimes.shape=}")
-    smoothglmderivratios = tide_filt.unpadvec(
-        smooth(tide_filt.padvec(glmderivratios, padlen=20, padtype="constant"), smoothpts),
-        padlen=20,
-    )
-    glmderivratios = glmderivratios[edgepad:-edgepad]
-    smoothglmderivratios = smoothglmderivratios[edgepad:-edgepad]
+    if glmderivs == 1:
+        smoothglmderivratios = tide_filt.unpadvec(
+            smooth(tide_filt.padvec(glmderivratios, padlen=20, padtype="constant"), smoothpts),
+            padlen=20,
+        )
+        glmderivratios = glmderivratios[edgepad:-edgepad]
+        smoothglmderivratios = smoothglmderivratios[edgepad:-edgepad]
+    else:
+        smoothglmderivratios = np.zeros_like(glmderivratios)
+        for i in range(glmderivs):
+            smoothglmderivratios[i, :] = tide_filt.unpadvec(
+                smooth(
+                    tide_filt.padvec(glmderivratios[i, :], padlen=20, padtype="constant"),
+                    smoothpts,
+                ),
+                padlen=20,
+            )
+        glmderivratios = glmderivratios[:, edgepad:-edgepad]
+        smoothglmderivratios = smoothglmderivratios[:, edgepad:-edgepad]
     lagtimes = lagtimes[edgepad:-edgepad]
     if debug:
         print("after trimming")
@@ -164,16 +180,6 @@ def trainratiotooffset(
     maplimits = (xaxis[0], xaxis[-1])
 
     if outputlevel != "min":
-        """tide_io.writebidstsv(
-            f"{outputname}_desc-ratiotodelaymapping_timeseries",
-            np.stack((xaxis, yaxis)),
-            1.0,
-            columns=["smoothglmderivratio", "delay"],
-            extraheaderinfo={
-                "Description": "The ratio of sLFO derivative to the sLFO, and the corresponding delay offset"
-            },
-            append=False,
-        )"""
         resampaxis = np.linspace(xaxis[0], xaxis[-1], num=len(xaxis), endpoint=True)
         tide_io.writebidstsv(
             f"{outputname}_desc-ratiotodelayfunc_timeseries",
@@ -181,9 +187,7 @@ def trainratiotooffset(
             1.0 / (resampaxis[1] - resampaxis[0]),
             starttime=resampaxis[0],
             columns=["delay"],
-            extraheaderinfo={
-                "Description": "The function mapping derivative ratio to delay"
-            },
+            extraheaderinfo={"Description": "The function mapping derivative ratio to delay"},
             append=False,
         )
 
@@ -198,6 +202,34 @@ def ratiotodelay(theratio):
         return ratiotooffsetfunc(theratio)
 
 
+def coffstodelay(thecoffs, mindelay=-3.0, maxdelay=3.0, debug=False):
+    justaone = np.array([1.0], dtype=thecoffs.dtype)
+    allcoffs = np.concatenate((justaone, thecoffs))
+    theroots = (poly.Polynomial(allcoffs, domain=(mindelay, maxdelay))).roots()
+    if theroots is None:
+        return 0.0
+    elif len(theroots) == 1:
+        return theroots[0].real
+    else:
+        candidates = []
+        for i in range(len(theroots)):
+            if np.isreal(theroots[i]) and (mindelay <= theroots[i] <= maxdelay):
+                if debug:
+                    print(f"keeping root {i} ({theroots[i]})")
+                candidates.append(theroots[i].real)
+            else:
+                if debug:
+                    print(f"discarding root {i} ({theroots[i]})")
+                else:
+                    pass
+        if len(candidates) > 0:
+            chosen = candidates[np.argmin(np.fabs(np.array(candidates)))].real
+            if debug:
+                print(f"{theroots=}, {candidates=}, {chosen=}")
+            return chosen
+        return 0.0
+
+
 def getderivratios(
     fmri_data_valid,
     validvoxels,
@@ -219,12 +251,14 @@ def getderivratios(
     LGR,
     TimingLGR,
     optiondict,
+    glmderivs=1,
     debug=False,
 ):
     if debug:
         print("getderivratios")
         print(f"{fitNorm.shape=}")
         print(f"{fitcoeff.shape=}")
+        print(f"{glmderivs=}")
     voxelsprocessed_glm, regressorset, evset = tide_glmfrommaps.glmfrommaps(
         fmri_data_valid,
         validvoxels,
@@ -249,7 +283,7 @@ def getderivratios(
         optiondict["saveminimumglmfiles"],
         nprocs_makelaggedtcs=optiondict["nprocs_makelaggedtcs"],
         nprocs_glm=optiondict["nprocs_glm"],
-        glmderivs=1,
+        glmderivs=glmderivs,
         mp_chunksize=optiondict["mp_chunksize"],
         showprogressbar=optiondict["showprogressbar"],
         alwaysmultiproc=optiondict["alwaysmultiproc"],
@@ -258,13 +292,19 @@ def getderivratios(
     )
 
     # calculate the ratio of the first derivative to the main regressor
-    glmderivratio = np.nan_to_num(fitcoeff[:, 1] / fitcoeff[:, 0])
+    if glmderivs == 1:
+        glmderivratios = np.nan_to_num(fitcoeff[:, 1] / fitcoeff[:, 0])
+    else:
+        numvoxels = fitcoeff.shape[0]
+        glmderivratios = np.zeros((glmderivs, numvoxels), dtype=np.float64)
+        for i in range(glmderivs):
+            glmderivratios[i, :] = np.nan_to_num(fitcoeff[:, i + 1] / fitcoeff[:, 0])
 
-    return glmderivratio
+    return glmderivratios
 
 
 def filterderivratios(
-    glmderivratio,
+    glmderivratios,
     nativespaceshape,
     validvoxels,
     thedims,
@@ -283,7 +323,7 @@ def filterderivratios(
         print(f"\t{nativespaceshape=}")
 
     # filter the ratio to find weird values
-    themad = mad(glmderivratio).astype(np.float64)
+    themad = mad(glmderivratios).astype(np.float64)
     print(f"MAD of GLM derivative ratios = {themad}")
     outmaparray, internalspaceshape = tide_io.makedestarray(
         nativespaceshape,
@@ -291,24 +331,24 @@ def filterderivratios(
         fileiscifti=fileiscifti,
         rt_floattype=rt_floattype,
     )
-    mappedglmderivratio = tide_io.populatemap(
-        glmderivratio,
+    mappedglmderivratios = tide_io.populatemap(
+        glmderivratios,
         internalspaceshape,
         validvoxels,
         outmaparray,
         debug=debug,
     )
     if textio or fileiscifti:
-        medfilt = glmderivratio
-        filteredarray = glmderivratio
+        medfilt = glmderivratios
+        filteredarray = glmderivratios
     else:
         if debug:
-            print(f"{glmderivratio.shape=}, {mappedglmderivratio.shape=}")
+            print(f"{glmderivratios.shape=}, {mappedglmderivratios.shape=}")
         medfilt = median_filter(
-            mappedglmderivratio.reshape(nativespaceshape), size=(3, 3, 3)
+            mappedglmderivratios.reshape(nativespaceshape), size=(3, 3, 3)
         ).reshape(internalspaceshape)[validvoxels]
         filteredarray = np.where(
-            np.fabs(glmderivratio - medfilt) > patchthresh * themad, medfilt, glmderivratio
+            np.fabs(glmderivratios - medfilt) > patchthresh * themad, medfilt, glmderivratios
         )
         if gausssigma > 0:
             mappedfilteredarray = tide_io.populatemap(

rapidtide/refineregressor.py

@@ -151,6 +151,9 @@ def alignvoxels(
     """
     inputshape = np.shape(fmridata)
     volumetotal = np.sum(lagmask)
+    if debug:
+        print("alignvoxels: {inputshape}")
+        print("volumetotal: {volumetotal}")
 
     # timeshift the valid voxels
     if nprocs > 1 or alwaysmultiproc:
@@ -253,6 +256,7 @@ def makerefinemask(
     bipolar=False,
     includemask=None,
     excludemask=None,
+    fixdelay=False,
     debug=False,
     rt_floatset=np.float64,
     rt_floattype="float64",
@@ -321,35 +325,45 @@ def makerefinemask(
         LGR.info(f"setting ampthresh to the {-100.0 * ampthresh}th percentile ({theampthresh})")
     else:
         theampthresh = ampthresh
+    if debug:
+        print(f"makerefinemask: {theampthresh=}")
     if bipolar:
         ampmask = np.where(np.fabs(lagstrengths) >= theampthresh, np.int16(1), np.int16(0))
     else:
         ampmask = np.where(lagstrengths >= theampthresh, np.int16(1), np.int16(0))
-    if lagmaskside == "upper":
-        delaymask = np.where(
-            (lagtimes - offsettime) > lagminthresh,
-            np.int16(1),
-            np.int16(0),
-        ) * np.where(
-            (lagtimes - offsettime) < lagmaxthresh,
-            np.int16(1),
-            np.int16(0),
-        )
-    elif lagmaskside == "lower":
-        delaymask = np.where(
-            (lagtimes - offsettime) < -lagminthresh,
-            np.int16(1),
-            np.int16(0),
-        ) * np.where(
-            (lagtimes - offsettime) > -lagmaxthresh,
-            np.int16(1),
-            np.int16(0),
-        )
+    if fixdelay:
+        delaymask = lagmask + 0
     else:
-        abslag = abs(lagtimes - offsettime)
-        delaymask = np.where(abslag > lagminthresh, np.int16(1), np.int16(0)) * np.where(
-            abslag < lagmaxthresh, np.int16(1), np.int16(0)
-        )
+        if lagmaskside == "upper":
+            delaymask = np.where(
+                (lagtimes - offsettime) > lagminthresh,
+                np.int16(1),
+                np.int16(0),
+            ) * np.where(
+                (lagtimes - offsettime) < lagmaxthresh,
+                np.int16(1),
+                np.int16(0),
+            )
+        elif lagmaskside == "lower":
+            delaymask = np.where(
+                (lagtimes - offsettime) < -lagminthresh,
+                np.int16(1),
+                np.int16(0),
+            ) * np.where(
+                (lagtimes - offsettime) > -lagmaxthresh,
+                np.int16(1),
+                np.int16(0),
+            )
+        else:
+            abslag = abs(lagtimes - offsettime)
+            delaymask = np.where(abslag > lagminthresh, np.int16(1), np.int16(0)) * np.where(
+                abslag < lagmaxthresh, np.int16(1), np.int16(0)
+            )
+        if debug:
+            print(f"makerefinemask: {lagmaskside=}")
+            print(f"makerefinemask: {lagminthresh=}")
+            print(f"makerefinemask: {lagmaxthresh=}")
+            print(f"makerefinemask: {offsettime=}")
     sigmamask = np.where(lagsigma < sigmathresh, np.int16(1), np.int16(0))
     locationmask = lagmask + 0
     if includemask is not None:

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/tidepoolTemplate.py

@@ -39,6 +39,7 @@ class Ui_MainWindow(object):
         self.logOutput.setGeometry(QtCore.QRect(10, 30, 651, 131))
         font = QtGui.QFont()
         font.setFamily("Courier")
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.imageData_groupBox = QtWidgets.QGroupBox(self.centralwidget)

rapidtide/tidepoolTemplate.ui

@@ -80,6 +80,7 @@
      <property name="font">
       <font>
        <family>Courier</family>
+       <bold>true</bold>
       </font>
      </property>
     </widget>

rapidtide/tidepoolTemplate_alt.py

@@ -14,14 +14,14 @@ from PyQt5 import QtCore, QtGui, QtWidgets
 class Ui_MainWindow(object):
     def setupUi(self, MainWindow):
         MainWindow.setObjectName("MainWindow")
-        MainWindow.resize(1380, 810)
+        MainWindow.resize(1375, 805)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
         sizePolicy.setHorizontalStretch(1)
         sizePolicy.setVerticalStretch(1)
         sizePolicy.setHeightForWidth(MainWindow.sizePolicy().hasHeightForWidth())
         MainWindow.setSizePolicy(sizePolicy)
-        MainWindow.setMinimumSize(QtCore.QSize(1380, 810))
-        MainWindow.setMaximumSize(QtCore.QSize(1380, 810))
+        MainWindow.setMinimumSize(QtCore.QSize(1375, 805))
+        MainWindow.setMaximumSize(QtCore.QSize(1375, 805))
         MainWindow.setSizeIncrement(QtCore.QSize(1, 1))
         self.centralwidget = QtWidgets.QWidget(MainWindow)
         self.centralwidget.setObjectName("centralwidget")
@@ -684,6 +684,7 @@ class Ui_MainWindow(object):
         font = QtGui.QFont()
         font.setFamily("Courier New")
         font.setPointSize(11)
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.simfunc_groupBox = QtWidgets.QGroupBox(self.centralwidget)
@@ -718,7 +719,7 @@ class Ui_MainWindow(object):
         self.simfunc_groupBox.raise_()
         MainWindow.setCentralWidget(self.centralwidget)
         self.menubar = QtWidgets.QMenuBar(MainWindow)
-        self.menubar.setGeometry(QtCore.QRect(0, 0, 1373, 24))
+        self.menubar.setGeometry(QtCore.QRect(0, 0, 1375, 24))
         self.menubar.setObjectName("menubar")
         MainWindow.setMenuBar(self.menubar)
         self.statusbar = QtWidgets.QStatusBar(MainWindow)

rapidtide/tidepoolTemplate_alt.ui

@@ -1766,6 +1766,7 @@
       <font>
        <family>Courier New</family>
        <pointsize>11</pointsize>
+       <bold>true</bold>
       </font>
      </property>
     </widget>
@@ -1847,7 +1848,7 @@
     <rect>
      <x>0</x>
      <y>0</y>
-     <width>1373</width>
+     <width>1375</width>
      <height>24</height>
     </rect>
    </property>
@@ -1891,7 +1892,7 @@
   </property>
  </designerdata>
  <buttongroups>
-  <buttongroup name="colormap_buttonGroup"/>
   <buttongroup name="stats_buttonGroup"/>
+  <buttongroup name="colormap_buttonGroup"/>
  </buttongroups>
 </ui>

rapidtide/tidepoolTemplate_alt_qt6.py

@@ -12,14 +12,14 @@ from PyQt6 import QtCore, QtGui, QtWidgets
 class Ui_MainWindow(object):
     def setupUi(self, MainWindow):
         MainWindow.setObjectName("MainWindow")
-        MainWindow.resize(1380, 810)
+        MainWindow.resize(1375, 805)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
         sizePolicy.setHorizontalStretch(1)
         sizePolicy.setVerticalStretch(1)
         sizePolicy.setHeightForWidth(MainWindow.sizePolicy().hasHeightForWidth())
         MainWindow.setSizePolicy(sizePolicy)
-        MainWindow.setMinimumSize(QtCore.QSize(1380, 810))
-        MainWindow.setMaximumSize(QtCore.QSize(1380, 810))
+        MainWindow.setMinimumSize(QtCore.QSize(1375, 805))
+        MainWindow.setMaximumSize(QtCore.QSize(1375, 805))
         MainWindow.setSizeIncrement(QtCore.QSize(1, 1))
         self.centralwidget = QtWidgets.QWidget(parent=MainWindow)
         self.centralwidget.setObjectName("centralwidget")
@@ -682,6 +682,7 @@ class Ui_MainWindow(object):
         font = QtGui.QFont()
         font.setFamily("Courier New")
         font.setPointSize(11)
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.simfunc_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
@@ -716,7 +717,7 @@ class Ui_MainWindow(object):
         self.simfunc_groupBox.raise_()
         MainWindow.setCentralWidget(self.centralwidget)
         self.menubar = QtWidgets.QMenuBar(parent=MainWindow)
-        self.menubar.setGeometry(QtCore.QRect(0, 0, 1373, 24))
+        self.menubar.setGeometry(QtCore.QRect(0, 0, 1375, 24))
         self.menubar.setObjectName("menubar")
         MainWindow.setMenuBar(self.menubar)
         self.statusbar = QtWidgets.QStatusBar(parent=MainWindow)

rapidtide/tidepoolTemplate_big.py

@@ -868,6 +868,7 @@ class Ui_MainWindow(object):
         font = QtGui.QFont()
         font.setFamily("Courier New")
         font.setPointSize(11)
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.simfunc_groupBox = QtWidgets.QGroupBox(self.centralwidget)

rapidtide/tidepoolTemplate_big.ui

@@ -2254,6 +2254,7 @@
       <font>
        <family>Courier New</family>
        <pointsize>11</pointsize>
+       <bold>true</bold>
       </font>
      </property>
     </widget>

rapidtide/tidepoolTemplate_big_qt6.py

@@ -866,6 +866,7 @@ class Ui_MainWindow(object):
         font = QtGui.QFont()
         font.setFamily("Courier New")
         font.setPointSize(11)
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.simfunc_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)

rapidtide/tidepoolTemplate_qt6.py

@@ -37,6 +37,7 @@ class Ui_MainWindow(object):
         self.logOutput.setGeometry(QtCore.QRect(10, 30, 651, 131))
         font = QtGui.QFont()
         font.setFamily("Courier")
+        font.setBold(True)
         self.logOutput.setFont(font)
         self.logOutput.setObjectName("logOutput")
         self.imageData_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)

rapidtide/workflows/parser_funcs.py

@@ -83,7 +83,7 @@ def invert_float(parser, arg):
     return arg
 
 
-def is_float(parser, arg):
+def is_float(parser, arg, minval=None, maxval=None):
     """
     Check if argument is float or auto.
     """
@@ -92,6 +92,10 @@ def is_float(parser, arg):
             arg = float(arg)
         except parser.error:
             parser.error('Value {0} is not a float or "auto"'.format(arg))
+        if minval is not None and arg < minval:
+            parser.error("Value {0} is smaller than {1}".format(arg, minval))
+        if maxval is not None and arg > maxval:
+            parser.error("Value {0} is larger than {1}".format(arg, maxval))
 
     return arg
 
@@ -115,7 +119,7 @@ def is_valid_file_or_float(parser, arg):
     return arg
 
 
-def is_int(parser, arg):
+def is_int(parser, arg, minval=None, maxval=None):
     """
     Check if argument is int or auto.
     """
@@ -124,6 +128,10 @@ def is_int(parser, arg):
             arg = int(arg)
         except parser.error:
             parser.error('Value {0} is not an int or "auto"'.format(arg))
+        if minval is not None and arg < minval:
+            parser.error("Value {0} is smaller than {1}".format(arg, minval))
+        if maxval is not None and arg > maxval:
+            parser.error("Value {0} is larger than {1}".format(arg, maxval))
 
     return arg