petpal 0.5.4__py3-none-any.whl → 0.5.6__py3-none-any.whl

petpal/cli/cli_preproc.py

@@ -345,89 +345,84 @@ def main():
         preproc_parser.print_help()
         raise SystemExit('Exiting without command')
 
-    if len(args.motion_target)==1:
-        motion_target = args.motion_target[0]
+    if 'motion_target' in dir(args):
+        if len(args.motion_target)==1:
+            motion_target = args.motion_target[0]
+        else:
+            motion_target = args.motion_target
     else:
-        motion_target = args.motion_target
+        motion_target = None
 
     command = str(args.command).replace('-','_')
 
-    if command=='weighted_series_sum':
-        useful_functions.weighted_series_sum(input_image_4d_path=args.input_img,
-                                             out_image_path=args.out_img,
-                                             half_life=args.half_life,
-                                             start_time=args.start_time,
-                                             end_time=args.end_time,
-                                             verbose=True)
-
-    if command=='auto_crop':
-        image_operations_4d.SimpleAutoImageCropper(input_image_path=args.input_img,
-                                                   out_image_path=args.out_img,
-                                                   thresh_val=args.thresh_val,
-                                                   verbose=True)
-
-    if command=='motion_correction':
-        motion_corr.motion_corr(input_image_4d_path=args.input_img,
+    match command:
+        case 'weighted_series_sum':
+            useful_functions.weighted_series_sum(input_image_4d_path=args.input_img,
+                                                 out_image_path=args.out_img,
+                                                 half_life=args.half_life,
+                                                 start_time=args.start_time,
+                                                 end_time=args.end_time,
+                                                 verbose=True)
+        case 'auto_crop':
+            image_operations_4d.SimpleAutoImageCropper(input_image_path=args.input_img,
+                                                    out_image_path=args.out_img,
+                                                    thresh_val=args.thresh_val,
+                                                    verbose=True)
+        case 'motion_correction':
+            motion_corr.motion_corr(input_image_4d_path=args.input_img,
+                                    out_image_path=args.out_img,
+                                    motion_target_option=motion_target,
+                                    verbose=True,
+                                    type_of_transform=args.transform_type,
+                                    half_life=args.half_life)
+        case 'register_pet':
+            register.register_pet(input_reg_image_path=args.input_img,
                                 out_image_path=args.out_img,
+                                reference_image_path=args.anatomical,
                                 motion_target_option=motion_target,
                                 verbose=True,
-                                type_of_transform=args.transform_type,
                                 half_life=args.half_life)
-    if command=='register_pet':
-        register.register_pet(input_reg_image_path=args.input_img,
-                              out_image_path=args.out_img,
-                              reference_image_path=args.anatomical,
-                              motion_target_option=motion_target,
-                              verbose=True,
-                              half_life=args.half_life)
-
-    if command=='write_tacs_old':
-        regional_tac_extraction.write_tacs(input_image_path=args.input_img,
-                                           out_tac_dir=args.out_tac_dir,
-                                           segmentation_image_path=args.segmentation,
-                                           label_map_path=args.label_map_path,
-                                           verbose=True)
-
-    if command=='write_tacs':
-        tac_obj = regional_tac_extraction.WriteRegionalTacs(input_image_path=args.input_img,
-                                                  segmentation_path=args.segmentation,
-                                                  label_map=args.label_map)
-        tac_obj(out_tac_prefix=args.patid,
-                out_tac_dir=args.out_tac_dir,
-                one_tsv_per_region=not args.excel)
-
-    if command=='warp_pet_atlas':
-        register.warp_pet_atlas(input_image_path=args.input_img,
-                                anat_image_path=args.anatomical,
-                                atlas_image_path=args.reference_atlas,
-                                out_image_path=args.out_img,
-                                verbose=True)
-
-    if command=='gauss_blur':
-        image_operations_4d.gauss_blur(input_image_path=args.input_img,
-                                       blur_size_mm=args.blur_size_mm,
+        case 'write_tacs_old':
+            regional_tac_extraction.write_tacs(input_image_path=args.input_img,
+                                            out_tac_dir=args.out_tac_dir,
+                                            segmentation_image_path=args.segmentation,
+                                            label_map_path=args.label_map_path,
+                                            verbose=True)
+        case 'write_tacs':
+            tac_obj = regional_tac_extraction.WriteRegionalTacs(input_image_path=args.input_img,
+                                                    segmentation_path=args.segmentation,
+                                                    label_map=args.label_map)
+            tac_obj(out_tac_prefix=args.patid,
+                    out_tac_dir=args.out_tac_dir,
+                    one_tsv_per_region=not args.excel)
+        case 'warp_pet_atlas':
+            register.warp_pet_to_atlas(input_image_path=args.input_img,
+                                       anat_image_path=args.anatomical,
+                                       atlas_image_path=args.reference_atlas,
                                        out_image_path=args.out_img,
-                                       verbose=True,
-                                       use_fwhm=True)
-
-    if command=='suvr':
-        image_operations_4d.suvr(input_image_path=args.input_img,
-                                 out_image_path=args.out_img,
-                                 segmentation_image_path=args.segmentation,
-                                 ref_region=args.ref_region)
-
-    if command=='windowed_motion_corr':
-        motion_corr.windowed_motion_corr_to_target(input_image_path=args.input_img,
-                                                   out_image_path=args.out_img,
-                                                   motion_target_option=motion_target,
-                                                   w_size=args.window_size,
-                                                   type_of_transform=args.transform_type)
-
-    if command=='rescale_image':
-        input_img = ants.image_read(filename=args.input_img)
-        out_img = image_operations_4d.rescale_image(input_image=input_img,
-                                                    rescale_constant=args.scale_factor)
-        ants.image_write(image=out_img, filename=args.out_img)
+                                       verbose=True)
+        case 'gauss_blur':
+            image_operations_4d.gauss_blur(input_image_path=args.input_img,
+                                        blur_size_mm=args.blur_size_mm,
+                                        out_image_path=args.out_img,
+                                        verbose=True,
+                                        use_fwhm=True)
+        case 'suvr':
+            image_operations_4d.suvr(input_image_path=args.input_img,
+                                     out_image_path=args.out_img,
+                                     segmentation_image_path=args.segmentation,
+                                     ref_region=args.ref_region)
+        case 'windowed_motion_corr':
+            motion_corr.windowed_motion_corr_to_target(input_image_path=args.input_img,
+                                                    out_image_path=args.out_img,
+                                                    motion_target_option=motion_target,
+                                                    w_size=args.window_size,
+                                                    type_of_transform=args.transform_type)
+        case 'rescale_image':
+            input_img = ants.image_read(filename=args.input_img)
+            out_img = image_operations_4d.rescale_image(input_image=input_img,
+                                                        rescale_constant=args.scale_factor)
+            ants.image_write(image=out_img, filename=args.out_img)
 
 if __name__ == "__main__":
     main()

petpal/kinetic_modeling/graphical_analysis.py

@@ -91,6 +91,50 @@ def fit_line_to_data_using_lls_with_rsquared(xdata: np.ndarray,
     return fit_ans[0][0], fit_ans[0][1], r_squared
 
 
+@numba.njit()
+def linear_least_squares_fit_with_stats(xdata: np.ndarray,
+                                        ydata: np.ndarray) -> tuple[float, float, float, float, float]:
+    """Fits a line to the data using least squares and explicitly computes:
+        - Fit R^2
+        - Standard error of the intercept
+        - Standard error of the slope
+
+    Args:
+        xdata (np.ndarray): X-coordinates of the data.
+        ydata (np.ndarray): Y-coordinates of the data.
+
+    Returns:
+        tuple: A tuple containing five float values: the intercept of the fitted line, the slope
+        of the fitted line, the r-squared value, the intercept standard error, and the slope
+        standard error.
+
+    See:
+        - https://mathworld.wolfram.com/LeastSquaresFitting.html
+    """
+    make_2d_matrix = _line_fitting_make_rhs_matrix_from_xdata
+    matrix = make_2d_matrix(xdata)
+    fit_ans = np.linalg.lstsq(matrix, ydata)
+
+    x_mean = np.mean(xdata)
+    y_mean = np.mean(ydata)
+
+    ss_res = fit_ans[1][0]
+    ss_tot = np.sum((y_mean - ydata) ** 2.)
+
+    n = len(xdata)
+
+    sum_square_xdiff = np.sum(xdata**2)-n*x_mean**2
+    sum_square_ydiff = np.sum(ydata**2)-n*y_mean**2
+    sum_square_xydiff = np.sum(xdata*ydata)-n*y_mean*x_mean
+
+    s = np.sqrt((sum_square_ydiff-sum_square_xydiff**2/sum_square_xdiff)/(n-2))
+
+    r_squared = 1.0 - ss_res / ss_tot
+
+    se_intercept = s*np.sqrt(1/n+np.mean(xdata)**2/sum_square_xdiff)
+    se_slope = s*sum_square_xdiff**(-0.5)
+    return fit_ans[0][0], fit_ans[0][1], r_squared, se_intercept, se_slope
+
 @numba.njit()
 def cumulative_trapezoidal_integral(xdata: np.ndarray,
                                     ydata: np.ndarray,

{petpal-0.5.4.dist-info → petpal-0.5.6.dist-info}/METADATA

@@ -1,10 +1,9 @@
 Metadata-Version: 2.4
 Name: petpal
-Version: 0.5.4
+Version: 0.5.6
 Summary: PET-PAL (Positron Emission Tomography Processing and Analysis Library)
 Project-URL: Repository, https://github.com/PETPAL-WUSM/PETPAL.git
-Author: Bradley Judge
-Author-email: Furqan Dar <dar@wustl.edu>, Noah Goldman <noahg@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>
+Author-email: Noah Goldman <noahg@wustl.edu>, Bradley Judge <bjudge@wustl.edu>, Furqan Dar <dar@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>
 License-File: LICENSE
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Science/Research
@@ -45,7 +44,17 @@ Description-Content-Type: text/markdown
 
 ## Installation
 
-Currently, we only support building the package directly from source. Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
+### Using Pip
+
+The simplest way to install PETPAL is using pip. First, ensure you are using Python version >=3.12. Then, run the following:
+
+```shell
+pip install petpal
+```
+
+### Build from source
+
+Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
 
 ```shell
 pip install .  # Installs the package

{petpal-0.5.4.dist-info → petpal-0.5.6.dist-info}/RECORD

@@ -6,7 +6,7 @@ petpal/cli/cli_idif.py,sha256=6lh_kJHcGjlHDXZOvbiuHrNqpk5FovVV5_j7_dPHTHU,5145
 petpal/cli/cli_parametric_images.py,sha256=JBFb8QlxZoGOzqvCJPFuZ7czzGWntJP5ZcfeM5-QF4Y,7385
 petpal/cli/cli_pib_processing.py,sha256=6EjoY0wSJZ7PImgjV9PxlGPgcZkcZISvFh9ctsZW3Gw,6935
 petpal/cli/cli_plot_tacs.py,sha256=XycaYQQl9Jp5jqDp3QXOlVT2sXHYYpYSraEArxsfJec,6479
-petpal/cli/cli_preproc.py,sha256=H8yfAa_fGzhLcyAU8JSOEAxsIF_DN81Ek8iWGkGj63Q,20106
+petpal/cli/cli_preproc.py,sha256=_l4OoOnKUTgu0T5lT9ctZK1h5qj7yBZgtf0m0PK_HS0,20355
 petpal/cli/cli_pvc.py,sha256=DC0JZ6p1pkc5BDgQ006bi9y0Mz32ENrjUaOtSvFobP4,3967
 petpal/cli/cli_reference_tissue_models.py,sha256=18BlKN4rMehyFbdq_yr88oztqR99_gBtWKImhwf7CQY,13283
 petpal/cli/cli_stats.py,sha256=Mqbzc9yYo9SVAfxzaYbAbk7EheW472l1PY_ptlD1DOI,2050
@@ -19,7 +19,7 @@ petpal/input_function/idif_necktangle.py,sha256=o5kyAqyT4C6o7zELY4EjyHrkJyX1BWcx
 petpal/input_function/pca_guided_idif.py,sha256=MPB59K5Z5oyIunIWFqFQts61z647xawLNkv8wICrKYM,44821
 petpal/kinetic_modeling/__init__.py,sha256=tW4yRH3TwaXPwKPqdkrbQmSk9hjrF1yRkV_C59PPboQ,382
 petpal/kinetic_modeling/fit_tac_with_rtms.py,sha256=HpK7VWVCCNoSQABY9i28vYpZsMRmvgs4vdcM_ZbdaYE,20971
-petpal/kinetic_modeling/graphical_analysis.py,sha256=uq3cnBwPEcSccQb_vy6cSH1j3kI3GePYMvYehD5HZKs,49456
+petpal/kinetic_modeling/graphical_analysis.py,sha256=a7IOwYnG3Wao2XTjFgsPK563txm7s4lpMbaqUMQ5wUQ,51003
 petpal/kinetic_modeling/parametric_images.py,sha256=sXYracBFUtFyttO-6oiDAldnU8hPN6Y4vKOD1V-DnlE,47301
 petpal/kinetic_modeling/reference_tissue_models.py,sha256=FkLziIgtpA8tOL2gZJFg_nB8VPEBs40T7RsDAJ3nJ-A,39510
 petpal/kinetic_modeling/rtm_analysis.py,sha256=e3EuaHXml4PDALEczwyOPpnThINAGh41UKNlOQHAPqc,25945
@@ -63,8 +63,8 @@ petpal/visualizations/graphical_plots.py,sha256=ZCKUeLX2TAQscuHjA4bzlFm1bACHIyCw
 petpal/visualizations/image_visualization.py,sha256=Ob6TD4Q0pIrxi0m9SznK1TRWbX1Ea9Pt4wNMdRrTfTs,9124
 petpal/visualizations/qc_plots.py,sha256=iaCPe-LWWyM3OZzDPZodHZhP-z5fRdpUgaH7QS9VxPM,1243
 petpal/visualizations/tac_plots.py,sha256=zSGdptL-EnqhfDViAX8LFunln5a1b-NJ5ft7ZDcxQ38,15116
-petpal-0.5.4.dist-info/METADATA,sha256=hUe3oDjdNZ9hW9e8E_nnoo-9-2geYFMHjlWMAVcsLQ4,2478
-petpal-0.5.4.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-petpal-0.5.4.dist-info/entry_points.txt,sha256=-AAg5GCaTRuwcLR7QWKPuKyBo8mTEMzspRmcBwaPdLo,692
-petpal-0.5.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-petpal-0.5.4.dist-info/RECORD,,
+petpal-0.5.6.dist-info/METADATA,sha256=W0Fo_jDNeBMUBbXybn9HymGcieOEqygaZDqETObBvrw,2617
+petpal-0.5.6.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+petpal-0.5.6.dist-info/entry_points.txt,sha256=0SZmyXqBxKzQg2eerDA16n2BdUEXyixEm0_AUo2dFns,653
+petpal-0.5.6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+petpal-0.5.6.dist-info/RECORD,,

{petpal-0.5.4.dist-info → petpal-0.5.6.dist-info}/entry_points.txt

@@ -1,5 +1,4 @@
 [console_scripts]
-petpal-bids = petpal.cli.cli_bids:main
 petpal-graph-analysis = petpal.cli.cli_graphical_analysis:main
 petpal-graph-plot = petpal.cli.cli_graphical_plots:main
 petpal-parametric-image = petpal.cli.cli_parametric_images:main