rapidtide 3.0.11__py3-none-any.whl → 3.1__py3-none-any.whl

rapidtide/data/examples/src/testLD

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+import matplotlib.pyplot as plt
+import numpy as np
+import statsmodels.api as sma
+import statsmodels.tsa.stattools as smts
+from scipy import signal
+from statsmodels.tsa.ar_model import AutoReg
+
+import rapidtide.io as tide_io
+
+debug = True
+insamplerate, instarttime, incolumns, indata, incompressed, incolsource = tide_io.readbidstsv(
+            "../dst/sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json",
+            neednotexist=False,
+            debug=debug,
+        )
+print(f"{indata.shape=}")
+nlags = 15
+
+p = 2
+d = 0
+q = 0
+
+for i in range(indata.shape[0]):
+    sigma_v, arcoefs, pacf, sigma, phi = smts.levinson_durbin(indata[i, :], nlags=nlags, isacov=False)
+
+    print(f"{sigma_v=}")
+    print(f"{arcoefs=}")
+    print(f"{pacf=}")
+    print(f"{sigma=}")
+    print(f"{phi=}")
+
+    plt.plot(arcoefs)
+    plt.show()
+
+    plt.plot(pacf)
+    plt.show()
+
+    plt.plot(sigma)
+    plt.show()
+ 
+    ar_model = AutoReg(indata[i, :], lags=nlags)
+    ar_fit = ar_model.fit()
+    ar_params = ar_fit.params
+
+    # The prewhitening filter coefficients are 1 for the numerator and 
+    # (1, -ar_params[1]) for the denominator
+    b = [1]
+    a = np.insert(-ar_params[1:], 0, 1)
+
+    # 3. Apply the filter to prewhiten the signal
+    prewhitened_signal = signal.lfilter(b, a, indata[i, :])
+    plt.plot(indata[i, :] / np.std(indata[i, :]))
+    plt.plot(prewhitened_signal / np.std(prewhitened_signal))
+    plt.show()

rapidtide/data/examples/src/testalign

@@ -41,7 +41,7 @@ alignedvec, maxdelay, maxval, failreason = tide_corr.aligntcwithref(
 )
 print(f"{maxdelay=}, {maxval=}, {failreason=}")
 
-filteredvec, datatoremove, R, coffs = tide_fit.linfitfilt(fixedvec, alignedvec, debug=True)
+filteredvec, datatoremove, R, coffs, dummy = tide_fit.linfitfilt(fixedvec, alignedvec, debug=True)
 
 offset = 0.0
 plt.plot(xaxis, fixedvec + offset)

rapidtide/data/examples/src/testdelayvar

@@ -7,7 +7,6 @@ delayvar \
     --nprocs -1 \
     --windowsize 30 \
     --systemicfittype pca \
-    --trainrange -999 -999 \
     --pcacomponents 0.8 \
     --outputlevel max \
     --focaldebug \

rapidtide/data/examples/src/testfmri

@@ -14,8 +14,26 @@ rapidtide \
     --nofitfilt \
     --refinedelayeachpass \
     --similaritymetric correlation \
+    --nonumba \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_flexipass
+    ../dst/sub-RAPIDTIDETEST_nonumba
+
+rapidtide \
+    --spatialfilt 2.5 \
+    --nprocs -1 \
+    --searchrange -7.5 30 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    --cleanrefined \
+    --nofitfilt \
+    --refinedelayeachpass \
+    --similaritymetric correlation \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_numba
 
 #rapidtide \
     #--spatialfilt 2.5 \

rapidtide/data/examples/src/testglmfilt

@@ -35,7 +35,7 @@ noisevec = noiseamp * np.random.rand(arrlen)
 invec = datavec + noisevec
 
 filtered, datatoremove, R, outcoffs, outintercept = tide_fit.linfitfilt(
-    invec, evs, returnintercept=True, debug=True
+    invec, evs, debug=True
 )
 
 incoffs = [amp1, amp2, amp3]
@@ -60,7 +60,7 @@ plt.plot(datavec - datatoremove + offset)
 print(R)
 plt.show()
 
-filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec, evs[:, 0], debug=True)
+filtered, datatoremove, R, coffs, dummy = tide_fit.linfitfilt(invec, evs[:, 0], debug=True)
 
 """
 offset = 0.0
@@ -82,7 +82,7 @@ invec2 = (
     + noiseamp * np.random.rand(arrlen)
 )
 
-filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec2, evs, debug=True)
+filtered, datatoremove, R, coffs, dummy = tide_fit.linfitfilt(invec2, evs, debug=True)
 
 """
 offset = 0.0
@@ -118,7 +118,7 @@ print(R)
 plt.show()
 """
 
-filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec2, thenewevs, debug=True)
+filtered, datatoremove, R, coffs, dummy = tide_fit.linfitfilt(invec2, thenewevs, debug=True)
 """
 offset = 0.0
 plt.plot(invec2 + offset)
@@ -140,7 +140,7 @@ alignedev, maxdelay, maxval, failreason = tide_corr.aligntcwithref(
     verbose=True,
 )
 print(f"{maxdelay=}, {maxval=}, {failreason=}")
-filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec3, alignedev, debug=True)
+filtered, datatoremove, R, coffs, dummy = tide_fit.linfitfilt(invec3, alignedev, debug=True)
 offset = 0.0
 plt.plot(evs[:, 0])
 offset += 1.0

rapidtide/data/examples/src/testhappy

@@ -69,15 +69,37 @@
     #../dst/happy_mpdetrend_mpphaseproj_nocache \
     #--nprocs -1
 
+#happy \
+    #sub-HAPPYTEST.nii.gz \
+    #sub-HAPPYTEST.json \
+    #../dst/happy_mask \
+    #--processmask sub-HAPPYTEST_mask.nii.gz \
+    #--nprocs -1
+
+#    --motionfile sub-HAPPYTEST_mcf.par \
+
+#happy \
+    #sub-HAPPYTEST.nii.gz \
+    #sub-HAPPYTEST.json \
+    #../dst/happy \
+    #--increaseoutputlevel \
+    #--model model_cnn_pytorch \
+    #--usepytorch \
+    #--nprocs -1
+
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    ../dst/happy_mask \
-    --processmask sub-HAPPYTEST_mask.nii.gz \
+    ../dst/happy_pytorch \
+    --increaseoutputlevel \
+    --usenewvesselmethod \
     --nprocs -1
 
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    ../dst/happy \
+    ../dst/happy_tensorflow \
+    --increaseoutputlevel \
+    --usenewvesselmethod \
+    --usetensorflow \
     --nprocs -1

rapidtide/data/examples/src/testppgproc

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+applyppgproc \
+    ../dst/happy_desc-slicerescardfromfmri_timeseries \
+    ppgtest \
+    --process_noise 0.001 \
+    --hr_estimate 65.0 \
+    --qual_thresh 0.7 \
+    --display --debug
+
+applyppgproc \
+    ../dst/happy_desc-stdrescardfromfmri_timeseries \
+    ppgtest \
+    --process_noise 0.001 \
+    --hr_estimate 65.0 \
+    --qual_thresh 0.7 \
+    --display --debug

rapidtide/data/examples/src/testrolloff

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for STOP in 2 3 4 5 6 7 8
+do
+    filttc ../dst/happy_desc-stdrescardfromfmri_timeseries.json:cardiacfromfmri_25.0Hz \
+    ../dst/stopfreq_${STOP} \
+    --filterfreqs 0.0 1.0 \
+    --filterstopfreqs 0.0 ${STOP}
+done
+
+showtc ../dst/stopfreq*.json --format separate

rapidtide/data/models/model_cnn_pytorch/loss.txt

@@ -0,0 +1 @@
+model_cnn_w060_l19_fn50_fl05_e025_t4.0_ct0.72_s20_d1_relu_normaligned: Prediction Error: 0.6981142062735153 Raw Error: 0.3174055677061575

rapidtide/data/models/model_cnn_pytorch/model_meta.json

@@ -0,0 +1,68 @@
+{
+    "dofft":false,
+    "dropout_rate":0.3,
+    "excludethresh":4.0,
+    "loss":[
+        0.30441974932999954,
+        0.18183457710591377,
+        0.16851514196375392,
+        0.16202728616720213,
+        0.15842841755073914,
+        0.1564911107478273,
+        0.15509463905571252,
+        0.15409289958448344,
+        0.15318550205312645,
+        0.15253183263581233,
+        0.15208946124896972,
+        0.15148001061784444,
+        0.1511366076229774,
+        0.15075672873619086,
+        0.15030987919196231,
+        0.15001051545245542,
+        0.14959304444363847,
+        0.1489250477134567,
+        0.14856653524837954,
+        0.1484835542405594,
+        0.14787971300050565,
+        0.14812416058430558,
+        0.14733259612854405,
+        0.14742844921770373,
+        0.14675265647906208
+    ],
+    "modelname":"model_cnn_w060_l19_fn50_fl05_e025_t4.0_ct0.72_s20_d1_relu_normaligned",
+    "nettype":"cnn",
+    "num_epochs":25,
+    "num_layers":19,
+    "prediction_error":0.6981142062735153,
+    "raw_error":0.3174055677061575,
+    "train_arch":"darwin",
+    "usebadpts":false,
+    "val_loss":[
+        0.15530714135745477,
+        0.15717816753634092,
+        0.1481180809695145,
+        0.1516780706315205,
+        0.13553270055302258,
+        0.1337960820259719,
+        0.13654720783233643,
+        0.1334461883738123,
+        0.12724334592449255,
+        0.12903443785576985,
+        0.12892387956380844,
+        0.12977149404328445,
+        0.13186248186333427,
+        0.12963887345174263,
+        0.12839905814877872,
+        0.12711975148011898,
+        0.13404886912682962,
+        0.1291459808575696,
+        0.12991093941803636,
+        0.13404125077971096,
+        0.14513506406340107,
+        0.12982086087095326,
+        0.12413997182558323,
+        0.1283193161775326,
+        0.13076527128959525
+    ],
+    "window_size":60
+}

rapidtide/decorators.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2025 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+from typing import Callable
+
+# ----------------------------------------- Conditional imports ---------------------------------------
+donotbeaggressive = True
+
+try:
+    from numba import jit
+except ImportError:
+    donotusenumba = True
+else:
+    donotusenumba = False
+
+
+def getdecoratorvars():
+    return donotusenumba, donotbeaggressive
+
+
+def conditionaljit() -> Callable:
+    """
+    Wrap functions in jit if numba is enabled.
+
+    This function creates a decorator that conditionally applies Numba's jit
+    decorator to functions. If the `donotusenumba` flag is True, the original
+    function is returned unchanged. Otherwise, the function is compiled with
+    `jit(nopython=True)` for optimal performance.
+
+    Returns
+    -------
+    Callable
+        A decorator function that can be applied to other functions.
+
+    Notes
+    -----
+    This decorator provides a convenient way to conditionally enable Numba
+    compilation based on a global flag. It's useful for debugging and
+    development where you want to disable JIT compilation temporarily.
+
+    Examples
+    --------
+    >>> @conditionaljit()
+    ... def my_function(x):
+    ...     return x * 2
+    ...
+    >>> result = my_function(5)
+    >>> print(result)
+    10
+    """
+
+    def resdec(f):
+        if donotusenumba:
+            return f
+        return jit(f, nopython=True)
+
+    return resdec
+
+
+def conditionaljit2() -> Callable:
+    """Return a decorator that conditionally applies numba JIT compilation (conservative mode).
+
+    Returns
+    -------
+    decorator
+        A decorator that applies numba JIT compilation with nopython=True if numba
+        is enabled and aggressive optimization is allowed, otherwise returns the function unchanged.
+        This is more conservative than conditionaljit() as it also checks the donotbeaggressive flag.
+    """
+
+    def resdec(f):
+        if donotusenumba or donotbeaggressive:
+            return f
+        return jit(f, nopython=True)
+
+    return resdec