petpal 0.5.8__tar.gz → 0.5.10__tar.gz

{petpal-0.5.8 → petpal-0.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: petpal
-Version: 0.5.8
+Version: 0.5.10
 Summary: PET-PAL (Positron Emission Tomography Processing and Analysis Library)
 Project-URL: Repository, https://github.com/PETPAL-WUSM/PETPAL.git
 Author-email: Noah Goldman <noahg@wustl.edu>, Bradley Judge <bjudge@wustl.edu>, Furqan Dar <dar@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>

{petpal-0.5.8 → petpal-0.5.10}/petpal/cli/cli_graphical_analysis.py

@@ -59,7 +59,6 @@ def main():
     parser_multitac = subparsers.add_parser('graphical-analysis-multitac')
     _add_common_args(parser_multitac)
     parser_multitac.add_argument("-r", "--roi-tacs-dir", required=True, help="Path to directory containing ROI TTACs")
-    parser_multitac.add_argument("-x","--excel", action='store_true',help='Set to output an excel-compatible table in a single file.',default=False)
 
     args = parser.parse_args()
     command = str(args.command).replace('-','_')
@@ -90,7 +89,7 @@ def main():
                                                               output_filename_prefix=args.output_filename_prefix,
                                                               method=method,
                                                               fit_thresh_in_mins=args.threshold_in_mins)
-        graphical_analysis(one_file_per_region=not args.excel, **run_kwargs)
+        graphical_analysis(output_as_tsv=True, output_as_json=False, **run_kwargs)
 
     if args.print:
         for key, val in graphical_analysis.analysis_props.items():

{petpal-0.5.8 → petpal-0.5.10}/petpal/preproc/image_operations_4d.py

@@ -64,10 +64,9 @@ def stitch_broken_scans(input_image_path: str,
     try:
         noninitial_time_zeroes = [meta['TimeZero'] for meta in noninitial_image_metadata_dicts]
         actual_time_zero = initial_image_metadata['TimeZero']
-    except KeyError:
-        raise KeyError(f'.json sidecar for one of your input images does not contain required BIDS key "TimeZero". '
-                       f'Aborting...')
-
+    except KeyError as exc:
+        raise KeyError('.json sidecar for one of your input images does not contain required BIDS '
+                       'key "TimeZero".') from exc
     initial_scan_time = datetime.time.fromisoformat(actual_time_zero)
     placeholder_date = datetime.date.today()
     initial_scan_datetime = datetime.datetime.combine(date=placeholder_date,

{petpal-0.5.8 → petpal-0.5.10}/petpal/preproc/regional_tac_extraction.py

@@ -1,6 +1,7 @@
 """
 Regional TAC extraction
 """
+from warnings import warn
 import os
 from collections.abc import Callable
 import pathlib
@@ -345,6 +346,20 @@ class WriteRegionalTacs:
             region_name = f'UNK{label:>04}'
         return region_name
 
+    def is_empty_region(self,pet_masked_region: np.ndarray) -> bool:
+        """Check if masked PET region has zero matched voxels, or is all NaNs. In either case,
+        return True, otherwise return False.
+        
+        Args:
+            pet_masked_region (np.ndarray): Array of PET voxels masked to a specific region.
+            
+        Returns:
+            pet_masked_region_is_empty (bool): If True, input region is empty."""
+        if pet_masked_region.size==0:
+            return True
+        if np.all(np.isnan(pet_masked_region)):
+            return True
+        return False
 
     def extract_tac(self,region_mapping: int | list[int], **tac_calc_kwargs) -> TimeActivityCurve:
         """
@@ -359,15 +374,46 @@ class WriteRegionalTacs:
         """
         region_mask = combine_regions_as_mask(segmentation_img=self.seg_arr,
                                               label=region_mapping)
+
         pet_masked_region = apply_mask_4d(input_arr=self.pet_arr,
                                           mask_arr=region_mask)
-        extracted_tac, uncertainty = self.tac_extraction_func(pet_voxels=pet_masked_region,
-                                                              **tac_calc_kwargs)
+
+        is_region_empty = self.is_empty_region(pet_masked_region=pet_masked_region)
+        if is_region_empty:
+            extracted_tac = np.empty_like(self.scan_timing.center_in_mins)
+            extracted_tac.fill(np.nan)
+            uncertainty = extracted_tac.copy()
+        else:
+            extracted_tac, uncertainty = self.tac_extraction_func(pet_voxels=pet_masked_region,
+                                                                  **tac_calc_kwargs)
         region_tac = TimeActivityCurve(times=self.scan_timing.center_in_mins,
                                        activity=extracted_tac,
                                        uncertainty=uncertainty)
         return region_tac
 
+    def gen_tacs_data_frame(self) -> pd.DataFrame:
+        """Get empty data frame to store TACs. Sets first two columns to frame start and end
+        times, and remaining columns are named by region activity and uncertainty, based on the
+        regions included in the label map.
+        
+        Returns:
+            tacs_data (pd.DataFrame): Data frame with columns set for frame start and end time,
+            and activity and uncertainty for each included region. Frame start and end time
+            columns filled with scan timing data.
+        """
+        activity_uncertainty_column_names = []
+        for region_name in self.region_names:
+            activity_uncertainty_column_names.append(region_name)
+            activity_uncertainty_column_names.append(f'{region_name}_unc')
+        cols_list = ['frame_start(min)','frame_end(min)'] + activity_uncertainty_column_names
+        tacs_data = pd.DataFrame(columns=cols_list)
+
+        tacs_data['frame_start(min)'] = self.scan_timing.start_in_mins
+        tacs_data['frame_end(min)'] = self.scan_timing.end_in_mins
+
+        return tacs_data
+
+
 
     def write_tacs(self,
                    out_tac_prefix: str,
@@ -378,7 +424,8 @@ class WriteRegionalTacs:
         Function to write Tissue Activity Curves for each region, given a segmentation,
         4D PET image, and label map. Computes the average of the PET image within each
         region. Writes TACs in TSV format with region name, frame start time, frame end time, and
-        activity and uncertainty within each region.
+        activity and uncertainty within each region. Skips writing regions without any matched
+        voxels.
 
         Args:
             out_tac_prefix (str): Prefix for the output files, usually the BIDS subject and
@@ -387,22 +434,34 @@ class WriteRegionalTacs:
             one_tsv_per_region (bool): If True, write one TSV TAC file for each region in the
                 image. If False, write one TSV file with all TACs in the image.
             **tac_calc_kwargs: Additional keywords passed onto tac_extraction_func.
-        """
-        tacs_data = pd.DataFrame()
 
-        tacs_data['frame_start(min)'] = self.scan_timing.start_in_mins
-        tacs_data['frame_end(min)'] = self.scan_timing.end_in_mins
+        Raises:
+            Warning: for each region without any matched voxels, warn user that TAC is skipped.
+        """
+        tacs_data = self.gen_tacs_data_frame()
 
+        empty_regions = []
         for i,region_name in enumerate(self.region_names):
             mappings = self.region_maps[i]
             tac = self.extract_tac(region_mapping=mappings, **tac_calc_kwargs)
+            if tac.contains_any_nan:
+                empty_regions.append(region_name)
+                continue
             if one_tsv_per_region:
+                os.makedirs(out_tac_dir, exist_ok=True)
                 tac.to_tsv(filename=f'{out_tac_dir}/{out_tac_prefix}_seg-{region_name}_tac.tsv')
             else:
                 tacs_data[region_name] = tac.activity
                 tacs_data[f'{region_name}_unc'] = tac.uncertainty
 
+        if len(empty_regions)>0:
+            warn("Empty regions were found during tac extraction. TACs for the following regions "
+                 f"were not saved: {empty_regions}")
+            tacs_data.drop(empty_regions,axis=1,inplace=True)
+            tacs_data.drop([f'{region}_unc' for region in empty_regions],axis=1,inplace=True)
+
         if not one_tsv_per_region:
+            os.makedirs(out_tac_dir, exist_ok=True)
             tacs_data.to_csv(f'{out_tac_dir}/{out_tac_prefix}_multitacs.tsv', sep='\t', index=False)
 
     def __call__(self,

{petpal-0.5.8 → petpal-0.5.10}/petpal/preproc/segmentation_tools.py

@@ -14,7 +14,9 @@ import nibabel
 from nibabel import processing
 import pandas as pd
 
-from ..utils.useful_functions import gen_nd_image_based_on_image_list
+from ..utils.useful_functions import (gen_nd_image_based_on_image_list,
+                                      check_physical_space_for_ants_image_pair,
+                                      get_average_of_timeseries)
 from ..utils import math_lib
 
 
@@ -571,3 +573,28 @@ def unique_segmentation_labels(segmentation_img: ants.core.ANTsImage | np.ndarra
     if not zeroth_roi:
         labels = labels[labels != 0]
     return labels
+
+def seg_crop_to_pet_fov(pet_img: ants.ANTsImage,
+                        segmentation_img: ants.ANTsImage,
+                        pet_thresh_value: float=np.finfo(float).eps) -> ants.ANTsImage:
+    """Zero out segmentation values that lie outside of the PET FOV.
+    
+    Especially applicable to scanners with limited FOV (field of view). PET voxels with values less
+    than 1e-36 are considered outside of the FOV.
+    
+    Args:
+        pet_img (ants.ANTsImage): PET image in anatomical space used to crop segmentation
+        segmentation_img (ants.ANTsImage): Segmentation image in anatomical space such as
+            FreeSurfer to which FOV cropping is applied.
+        pet_thresh_value (float): Lower threshold for the PET image by which the segmentation image
+            is masked. Should be <<1. Default machine epsilon for `float`.
+
+    Returns:
+        segmentation_masked_img (ants.ANTsImage): Segmentation image masked to PET FOV.
+    """
+    if not check_physical_space_for_ants_image_pair(pet_img, segmentation_img):
+        raise ValueError("PET and segmentation image must share physical space.")
+    pet_mean_img = get_average_of_timeseries(input_image=pet_img)
+    pet_mask = ants.threshold_image(pet_mean_img, pet_thresh_value)
+    seg_masked = ants.mask_image(segmentation_img, pet_mask)
+    return seg_masked

{petpal-0.5.8 → petpal-0.5.10}/petpal/preproc/symmetric_geometric_transfer_matrix.py

@@ -9,6 +9,7 @@ import warnings
 import numpy as np
 from scipy.ndimage import gaussian_filter
 import ants
+import pandas as pd
 
 from ..meta.label_maps import LabelMapLoader
 from ..utils.useful_functions import check_physical_space_for_ants_image_pair
@@ -92,24 +93,33 @@ class Sgtm:
         elif self.input_image.dimension == 4:
             self.sgtm_result = self.run_sgtm_4d()
 
-    def save(self, output_path: str, out_tac_prefix: str | None = None):
+    def save(self, output_path: str, out_tac_prefix: str | None = None, one_tsv_per_region: bool = False):
         r"""Save sGTM results by writing the resulting array to one or more files.
 
-        The behavior depends on the input iamge provided. If input image is 3D, saves the average sGTM value for each
+        The behavior depends on the input image provided. If input image is 3D, saves the average sGTM value for each
         region in a TSV with one row per region. If input image is 4D, saves time series average values for each frame
-        within each region as a TAC file.
+        within each region. 4D operation saves a single file unless `one_tsv_per_region` is set to True.
 
         Args:
-            output_path (str): Path to save sGTM results. For 3D images, this should typically be a full path to a
-                .tsv file. For 4D images, this is the directory where the sGTM TACs will be saved.
+            output_path (str): Path to save sGTM results. For 3D images, this should typically be
+                the full path to a .tsv file. For 4D images, this is the directory where the sGTM
+                TACs will be saved.
             out_tac_prefix (Optional, str): Prefix of the TAC files. Typically, something like
                 ``'sub-001_ses-001_desc-sGTM'``. Defaults to None.
+            one_tsv_per_region (bool): If True, saves one tsv file for each unique region, as
+                opposed to one file containing all TACs if False. Default False.
         """
         if self.input_image.dimension == 3:
             self.save_results_3d(sgtm_result=self.sgtm_result, out_tsv_path=output_path)
         elif self.input_image.dimension == 4:
-            self.save_results_4d_tacs(sgtm_result=self.sgtm_result, out_tac_dir=output_path,
-                                      out_tac_prefix=out_tac_prefix)
+            if one_tsv_per_region:
+                self.save_results_4d_tacs(sgtm_result=self.sgtm_result,
+                                          out_tac_dir=output_path,
+                                          out_tac_prefix=out_tac_prefix)
+            else:
+                self.save_results_4d_multitacs(sgtm_result=self.sgtm_result,
+                                               out_tac_dir=output_path,
+                                               out_tac_prefix=out_tac_prefix)
 
     def __call__(self, output_path: str, out_tac_prefix: str | None = None):
         r"""Run sGTM and save results.
@@ -162,8 +172,20 @@ class Sgtm:
                           "segmentation to ensure this criteria is met, or use sGTM without "
                           "label map for automated complete region mapping.")
             seg_label_map = LabelMapLoader(label_map_option=self.label_map_option).label_map
-            region_index_map = list(seg_label_map.values())
-            region_short_names = list(seg_label_map.keys())
+            unique_mappings = unique_segmentation_labels(segmentation_img=self.segmentation_image,
+                                                       zeroth_roi=self.zeroth_roi)
+            region_index_map = []
+            region_short_names = []
+            label_map_labels = list(seg_label_map.keys())
+            label_map_mappings = list(seg_label_map.values())
+            for mapping in unique_mappings:
+                if mapping in label_map_mappings:
+                    id_mapping_index = label_map_mappings.index(mapping)
+                    region_index_map.append(label_map_mappings[id_mapping_index])
+                    region_short_names.append(label_map_labels[id_mapping_index])
+                else:
+                    region_index_map.append(mapping)
+                    region_short_names.append(f'UNK{mapping:05d}')
         return (region_index_map, region_short_names)
 
 
@@ -291,7 +313,6 @@ class Sgtm:
 
         return unique_labels, t_corrected, condition_number
 
-
     def run_sgtm_4d(self) -> np.ndarray:
         r"""Calculated partial volume corrected TACs on a 4D image by running sGTM on each frame in
         the 4D image.
@@ -326,7 +347,6 @@ class Sgtm:
 
         return np.asarray(frame_results)
 
-
     def save_results_3d(self, sgtm_result: tuple, out_tsv_path: str):
         r"""Saves the result of an sGTM calculation.
 
@@ -337,12 +357,10 @@ class Sgtm:
             sgtm_result (tuple): Output of :meth:`run_sgtm_3d`
             out_tsv_path (str): File path to which results are saved.
         """
-        sgtm_result_array = np.array([sgtm_result[0], sgtm_result[1]]).T
-        np.savetxt(out_tsv_path,sgtm_result_array,
-                   header='Region\tMean',
-                   fmt=['%.0f','%.2f'],
-                   comments='')
-
+        sgtm_result_to_write = pd.DataFrame(columns=['Region','Mean'])
+        sgtm_result_to_write['Region'] = self.unique_labels[1]
+        sgtm_result_to_write['Mean'] = sgtm_result[1]
+        sgtm_result_to_write.to_csv(out_tsv_path,sep='\t',index=False)
 
     def save_results_4d_tacs(self,
                              sgtm_result: np.ndarray,
@@ -368,3 +386,31 @@ class Sgtm:
                                         activity=tac_array[i,:])
             out_tac_path = os.path.join(f'{out_tac_dir}', f'{out_tac_prefix}_seg-{name}_tac.tsv')
             pvc_tac.to_tsv(filename=out_tac_path)
+
+    def save_results_4d_multitacs(self,
+                                  sgtm_result: np.ndarray,
+                                  out_tac_dir: str,
+                                  out_tac_prefix: str):
+        """Like :meth:`save_results_4d_tacs`, but saves all TACs to a single file.
+
+        Args:
+            sgtm_result (np.ndarray): Array of results from :meth:`run_sgtm_4d`
+            out_tac_dir (str): Path to folder where regional TACs will be saved.
+            out_tac_prefix (str): Prefix of the TAC files.
+        """
+        os.makedirs(out_tac_dir, exist_ok=True)
+        input_image_path = self.input_image_path
+        scan_timing = ScanTimingInfo.from_nifti(image_path=input_image_path)
+        tac_time_starts = scan_timing.start_in_mins
+        tac_time_ends = scan_timing.end_in_mins
+
+        tac_array = np.asarray(sgtm_result).T
+        tacs_data_columns = ['frame_start(min)','frame_end(min)']+self.unique_labels[1]
+        tacs_data = pd.DataFrame(columns=tacs_data_columns)
+
+        tacs_data['frame_start(min)'] = tac_time_starts
+        tacs_data['frame_end(min)'] = tac_time_ends
+        for i, (_label, name) in enumerate(zip(*self.unique_labels)):
+            tacs_data[name] = tac_array[i,:]
+            tacs_data[f'{name}_unc'] = np.full(tac_array.shape[1],np.nan)
+        tacs_data.to_csv(f'{out_tac_dir}/{out_tac_prefix}_multitacs.tsv', sep='\t', index=False)

{petpal-0.5.8 → petpal-0.5.10}/petpal/utils/time_activity_curve.py

@@ -75,6 +75,7 @@ class TimeActivityCurve:
         return len(self.times)
 
     def __post_init__(self):
+        self.validate_activity()
         if self.uncertainty.size == 0:
             self.uncertainty = np.empty_like(self.times)
             self.uncertainty[:] = np.nan
@@ -82,6 +83,33 @@ class TimeActivityCurve:
             f"TAC fields must have the same shapes.\ntimes:{self.times.shape}"
             "activity:{self.activity.shape} uncertainty:{self.uncertainty.shape}")
 
+    def validate_activity(self):
+        """Validates that the activity attribute is defined correctly.
+        
+        `self.activity` must have the following properties:
+        1) It must exist and not be None
+        2) It must be a numpy array
+        3) It must have dtype float
+        4) It must be 1D
+
+        This function raises a ValueError if self.activity does not meet the first criteria, and
+        attempts to coerce self.activity into a 1D, numeric numpy array with dtype float if
+        criteria 2-4 are not met.
+        """
+        if not hasattr(self, "activity") or self.activity is None:
+            raise ValueError("TimeActivityCurve.activity must be provided and not be None")
+
+        try:
+            arr = np.asarray(self.activity, dtype=float)
+        except (TypeError, ValueError) as exc:
+            error_message = "TimeActivityCurve.activity must be numeric or convertible to numeric"
+            raise TypeError(error_message) from exc
+
+        if arr.ndim != 1:
+            arr = arr.ravel()
+
+        self.activity = arr
+
     @classmethod
     def from_tsv(cls, filename: str):
         """
@@ -509,29 +537,29 @@ class TimeActivityCurve:
                                                           kind='linear',
                                                           fill_value='extrapolate')(tac.times)
             return TimeActivityCurve(tac.times, shifted_vals_on_tac_times)
-        else:
-            return shifted_tac
+        return shifted_tac
 
     @staticmethod
     def tac_dispersion(tac: 'TimeActivityCurve',
-                       disp_func: Callable[[np.ndarray, ...], np.ndarray],
+                       disp_func: Callable[..., np.ndarray],
                        disp_kwargs: dict,
                        num_samples: int = 4096):
         r"""
         Applies a dispersion function to a time-activity curve (TAC) and returns the convolved TAC.
 
-        This method evaluates the specified dispersion function `disp_func` at supersampled time points.
-        It performs convolution (using :func:`scipy.signal.convolve`)of the supersampled TAC with
-        the dispersion function, and the result is sampled back at the original TAC time points
-        to form the new convolved TAC.
+        This method evaluates the specified dispersion function `disp_func` at supersampled time
+        points. It performs convolution (using :func:`scipy.signal.convolve`) of the supersampled
+        TAC with the dispersion function, and the result is sampled back at the original TAC time
+        points to form the new convolved TAC.
 
         .. note::
-            We perform the supersampling to ensure that the TACs are sampled evenly before performing
-            the convolution. Convolving non-evenly sampled arrays produces nonsense values.
+            We perform the supersampling to ensure that the TACs are sampled evenly before
+            performing the convolution. Convolving non-evenly sampled arrays produces nonsense
+            values.
 
         Args:
             tac (TimeActivityCurve): The original time-activity curve to be convolved.
-            disp_func (Callable[[np.ndarray, ...], np.ndarray]):
+            disp_func (Callable[..., np.ndarray]):
                 The dispersion function to be applied. This function must accept an array of
                 times as its first argument, followed by any additional arguments specified
                 in `disp_kwargs`.
@@ -541,8 +569,8 @@ class TimeActivityCurve:
                 Defaults to 4096.
 
         Returns:
-            TimeActivityCurve: A new `TimeActivityCurve` instance with the convolved activity values,
-            resampled at the original TAC time points.
+            TimeActivityCurve: A new `TimeActivityCurve` instance with the convolved activity
+            values, resampled at the original TAC time points.
 
         Example:
             .. code-block:: python
@@ -592,6 +620,12 @@ class TimeActivityCurve:
 
         return disp_tac.set_activity_non_negative()
 
+    @property
+    def contains_any_nan(self):
+        """Return True if TAC has any NaN activity values."""
+        any_nan = np.isnan(self.activity).any()
+        return any_nan
+
 def safe_load_tac(filename: str,
                   with_uncertainty: bool = False,
                   **kwargs) -> np.ndarray:

{petpal-0.5.8 → petpal-0.5.10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "petpal"
-version = "0.5.8"
+version = "0.5.10"
 description = "PET-PAL (Positron Emission Tomography Processing and Analysis Library)"
 authors = [
     {name = "Noah Goldman", email = "noahg@wustl.edu"},

petpal-0.5.10/tests/test_graphical_analysis.py

@@ -0,0 +1,90 @@
+import os
+import warnings
+import pytest
+import pandas as pd
+
+from petpal.utils.image_io import flatten_metadata
+import petpal.kinetic_modeling.graphical_analysis as ga
+
+def _make_instance(rsquared):
+    inst = ga.MultiTACGraphicalAnalysis.__new__(ga.MultiTACGraphicalAnalysis)
+    inst.analysis_props = [{'RSquared': rsquared}]
+    inst.output_directory = "/tmp"
+    inst.output_filename_prefix = "prefix"
+    inst.method = "patlak"
+    inst.inferred_seg_labels = ["roi1", "roi2"]
+    return inst
+
+
+def test_save_analysis_raises_if_run_not_called():
+    inst = _make_instance(rsquared=None)
+    with pytest.raises(RuntimeError):
+        inst.save_analysis()
+
+def test_save_analysis_calls_tsv_and_json(monkeypatch):
+    inst = _make_instance(rsquared=0.95)
+    calls = {"tsv": 0, "json": 0}
+
+    def km_multifit_analysis_to_tsv_without_save_file(analysis_props: list[dict],
+                                    output_directory: str,
+                                    output_filename_prefix: str,
+                                    method: str,
+                                    inferred_seg_labels: list[str]):
+        filename = f'{output_filename_prefix}_desc-{method}_fitprops.tsv'
+        filepath = os.path.join(output_directory, filename)
+        fit_table = pd.DataFrame()
+        for seg_name, fit_props in zip(inferred_seg_labels, analysis_props):
+            tmp_table = pd.DataFrame(flatten_metadata(fit_props),index=[seg_name])
+            fit_table = pd.concat([fit_table,tmp_table])
+        calls["tsv"] += 1
+        assert isinstance(analysis_props, list)
+        assert isinstance(output_directory, str)
+        assert isinstance(output_filename_prefix, str)
+        assert isinstance(method, str)
+        assert isinstance(inferred_seg_labels, list)
+
+    def km_multifit_analysis_to_jsons_without_save_file(analysis_props: list[dict],
+                                    output_directory: str,
+                                    output_filename_prefix: str,
+                                    method: str,
+                                    inferred_seg_labels: list[str]):
+        for seg_name, fit_props in zip(inferred_seg_labels, analysis_props):
+            filename = [output_filename_prefix,
+                        f'desc-{method}',
+                        f'seg-{seg_name}',
+                        'fitprops.json']
+            filename = '_'.join(filename)
+            filepath = os.path.join(output_directory, filename)
+        calls["json"] += 1
+        assert isinstance(analysis_props, list)
+        assert isinstance(output_directory, str)
+        assert isinstance(output_filename_prefix, str)
+        assert isinstance(method, str)
+        assert isinstance(inferred_seg_labels, list)
+
+    monkeypatch.setattr(ga, "km_multifit_analysis_to_tsv", km_multifit_analysis_to_tsv_without_save_file)
+    monkeypatch.setattr(ga, "km_multifit_analysis_to_jsons", km_multifit_analysis_to_jsons_without_save_file)
+
+    # Default behavior: TSV only
+    calls["tsv"] = calls["json"] = 0
+    inst.save_analysis(output_as_tsv=True, output_as_json=False)
+    assert calls["tsv"] == 1 and calls["json"] == 0
+
+    # JSON only
+    calls["tsv"] = calls["json"] = 0
+    inst.save_analysis(output_as_tsv=False, output_as_json=True)
+    assert calls["tsv"] == 0 and calls["json"] == 1
+
+    # Both
+    calls["tsv"] = calls["json"] = 0
+    inst.save_analysis(output_as_tsv=True, output_as_json=True)
+    assert calls["tsv"] == 1 and calls["json"] == 1
+
+def test_save_analysis_warns_when_no_output_requested(monkeypatch):
+    inst = _make_instance(rsquared=0.5)
+    # prevent actual functions being called if mistakenly invoked
+    monkeypatch.setattr(ga, "km_multifit_analysis_to_tsv", lambda *a, **k: (_ for _ in ()).throw(AssertionError("should not be called")))
+    monkeypatch.setattr(ga, "km_multifit_analysis_to_jsons", lambda *a, **k: (_ for _ in ()).throw(AssertionError("should not be called")))
+
+    with pytest.warns(UserWarning):
+        inst.save_analysis(output_as_tsv=False, output_as_json=False)

petpal-0.5.10/tests/test_sgtm.py

@@ -0,0 +1,53 @@
+import pytest
+from petpal.preproc.symmetric_geometric_transfer_matrix import Sgtm
+
+class DummyImage:
+    def __init__(self, dimension):
+        self.dimension = dimension
+
+def make_sgtm_with_dimension(dim, sgtm_result=None):
+    sgtm = object.__new__(Sgtm)
+    sgtm.input_image = DummyImage(dimension=dim)
+    sgtm.sgtm_result = sgtm_result
+    return sgtm
+
+def test_save_calls_save_results_3d_for_3d_image():
+    sgtm = make_sgtm_with_dimension(3, sgtm_result=("labels", "vals", 1.0))
+    called = {}
+    def fake_save_results_3d(sgtm_result, out_tsv_path):
+        called['args'] = (sgtm_result, out_tsv_path)
+    sgtm.save_results_3d = fake_save_results_3d
+
+    sgtm.save(output_path="out.tsv")
+
+    assert 'args' in called
+    assert called['args'][0] is sgtm.sgtm_result
+    assert called['args'][1] == "out.tsv"
+
+def test_save_calls_save_results_4d_tacs_when_one_tsv_per_region_true():
+    sgtm = make_sgtm_with_dimension(4, sgtm_result="frame_results")
+    called = {}
+    def fake_save_results_4d_tacs(sgtm_result, out_tac_dir, out_tac_prefix):
+        called['args'] = (sgtm_result, out_tac_dir, out_tac_prefix)
+    sgtm.save_results_4d_tacs = fake_save_results_4d_tacs
+
+    sgtm.save(output_path="/tmp/dir", out_tac_prefix="pref", one_tsv_per_region=True)
+
+    assert 'args' in called
+    assert called['args'][0] is sgtm.sgtm_result
+    assert called['args'][1] == "/tmp/dir"
+    assert called['args'][2] == "pref"
+
+def test_save_calls_save_results_4d_multitacs_when_one_tsv_per_region_false():
+    sgtm = make_sgtm_with_dimension(4, sgtm_result="frame_results")
+    called = {}
+    def fake_save_results_4d_multitacs(sgtm_result, out_tac_dir, out_tac_prefix):
+        called['args'] = (sgtm_result, out_tac_dir, out_tac_prefix)
+    sgtm.save_results_4d_multitacs = fake_save_results_4d_multitacs
+
+    sgtm.save(output_path="/tmp/dir2", out_tac_prefix="pref2", one_tsv_per_region=False)
+
+    assert 'args' in called
+    assert called['args'][0] is sgtm.sgtm_result
+    assert called['args'][1] == "/tmp/dir2"
+    assert called['args'][2] == "pref2"

petpal-0.5.10/tests/test_time_activity_curve.py

@@ -0,0 +1,33 @@
+import pytest
+import numpy as np
+from petpal.utils.time_activity_curve import TimeActivityCurve
+
+def test_post_init_sets_uncertainty_when_missing_and_converts_activity_to_float():
+    times = np.array([0.0, 10.0, 20.0])
+    activity = [1, 2, 3]  # list input should be converted to 1D float array
+    tac = TimeActivityCurve(times=times, activity=activity)
+    assert isinstance(tac.uncertainty, np.ndarray)
+    assert tac.uncertainty.shape == times.shape
+    assert np.all(np.isnan(tac.uncertainty))
+    assert tac.activity.dtype == float
+    assert tac.activity.shape == times.shape
+
+def test_post_init_raises_when_activity_is_none():
+    times = np.array([0.0, 5.0])
+    with pytest.raises(ValueError):
+        TimeActivityCurve(times=times, activity=None)
+
+def test_post_init_asserts_on_shape_mismatch_between_fields():
+    times = np.array([0.0, 10.0, 20.0])
+    activity = np.array([1.0, 2.0])  # different shape -> should trigger assertion
+    with pytest.raises(AssertionError):
+        TimeActivityCurve(times=times, activity=activity)
+
+def test_post_init_flattens_multidimensional_activity_to_1d_float():
+    times = np.array([0.0, 10.0, 20.0])
+    activity = np.array([[1, 2, 3]], dtype=int)  # 2D input should be ravelled and cast to float
+    tac = TimeActivityCurve(times=times, activity=activity)
+    assert tac.activity.ndim == 1
+    assert tac.activity.shape == times.shape
+    assert tac.activity.dtype == float
+    assert np.allclose(tac.activity, np.array([1.0, 2.0, 3.0]))