petpal 0.5.7__py3-none-any.whl → 0.5.8__py3-none-any.whl

petpal/preproc/decay_correction.py

@@ -129,21 +129,22 @@ def decay_correct(input_image_path: str,
     return corrected_image
 
 
-def calculate_frame_decay_factor(frame_reference_time: float,
-                                 half_life: float) -> float:
-    """Calculate decay factor for a single frame, given the frame reference time and half life.
+def calculate_frame_decay_factor(frame_reference_time: np.ndarray,
+                                 half_life: float) -> np.ndarray:
+    """Calculate decay correction factors for a scan given the frame reference time and half life.
     
     Important: 
         The frame reference time should be the time at which average activity occurs,
-        not simply the midpoint. See preproc.scan_timing.calculate_frame_reference_time for more info.
-        
+        not simply the midpoint. See
+        :meth:`~petpal.utils.scan_timing.calculate_frame_reference_time` for more info.
+
     Args: 
-        frame_reference_time (float): Time at which the average activity occurs for the frame.
+        frame_reference_time (np.ndarray): Time at which the average activity occurs for the frame.
         half_life (float): Radionuclide half life.
 
     Returns: 
-        float: Decay Correction Factor for the frame.     
+        np.ndarray: Decay Correction Factors for each frame in the scan.
     """
-    decay_constant = math.log(2)/half_life
-    frame_decay_factor = math.exp((decay_constant)*frame_reference_time)
-    return frame_decay_factor
+    decay_constant = np.log(2)/half_life
+    frame_decay_factor = np.exp((decay_constant)*frame_reference_time)
+    return frame_decay_factor

petpal/utils/scan_timing.py

@@ -1,7 +1,7 @@
 """
 Module to handle timing information of PET scans.
 """
-import math
+from typing import Self
 from dataclasses import dataclass
 import numpy as np
 
@@ -82,8 +82,8 @@ class ScanTimingInfo:
 
     """
     duration: np.ndarray[float]
-    end: np.ndarray[float]
     start: np.ndarray[float]
+    end: np.ndarray[float]
     center: np.ndarray[float]
     decay: np.ndarray[float]
 
@@ -130,7 +130,7 @@ class ScanTimingInfo:
 
 
     @classmethod
-    def from_metadata(cls, metadata_dict: dict):
+    def from_metadata(cls, metadata_dict: dict) -> Self:
         r"""
         Extracts frame timing information and decay factors from a json metadata.
         Expects that the JSON metadata has ``FrameDuration`` and ``DecayFactor`` or
@@ -155,13 +155,13 @@ class ScanTimingInfo:
         """
         frm_dur = np.asarray(metadata_dict['FrameDuration'], float)
         try:
-            frm_ends = np.asarray(metadata_dict['FrameTimesEnd'], float)
+            frm_starts = np.asarray(metadata_dict['FrameTimesStart'], float)
         except KeyError:
-            frm_ends = np.cumsum(frm_dur)
+            frm_starts = np.cumsum(frm_dur)-frm_dur
         try:
-            frm_starts = np.asarray(metadata_dict['FrameTimesStart'], float)
+            frm_ends = np.asarray(metadata_dict['FrameTimesEnd'], float)
         except KeyError:
-            frm_starts = np.diff(frm_ends)
+            frm_ends = frm_starts+frm_dur
         try:
             decay = np.asarray(metadata_dict['DecayCorrectionFactor'], float)
         except KeyError:
@@ -178,7 +178,7 @@ class ScanTimingInfo:
                    decay=decay)
 
     @classmethod
-    def from_nifti(cls, image_path: str):
+    def from_nifti(cls, image_path: str) -> Self:
         r"""
         Extracts frame timing information and decay factors from a NIfTI image metadata.
         Expects that the JSON metadata file has ``FrameDuration`` and ``DecayFactor`` or
@@ -204,6 +204,49 @@ class ScanTimingInfo:
         _meta_data = load_metadata_for_nifti_with_same_filename(image_path=image_path)
         return cls.from_metadata(metadata_dict=_meta_data)
 
+    @classmethod
+    def from_start_end(cls,
+                       frame_starts: np.ndarray,
+                       frame_ends: np.ndarray,
+                       decay_correction_factor: np.ndarray | None=None) -> Self:
+        """Infer timing properties based on start and end time.
+        
+        Args:
+            frame_starts (np.ndarray): Start time of each frame.
+            frame_ends (np.ndarray): End time of each frame.
+            decay_correction_factor (np.ndarray | None): Decay correction factor, which can be
+                optionally provided based on the type of analysis being done. If None, frame decay
+                will be set to ones. Default None.
+
+        Returns:
+            scan_timing_info (ScanTimingInfo): ScanTimingInfo object with the correct start, end,
+                duration, midpoint, and (optionally) decay correction for each frame.
+
+        Raises:
+            ValueError: If frame_starts, frame_ends, and decay_correction_factor (if provided) are
+                not of identical shape.
+
+        """
+        if frame_starts.shape != frame_ends.shape:
+            raise ValueError("frame_ends must have the same shape as frame_starts")
+
+        frame_duration = frame_ends - frame_starts
+        frame_midpoint = frame_starts + frame_duration / 2
+        frame_decay = np.ones_like(frame_starts)
+
+        if decay_correction_factor is None:
+            frame_decay = np.ones_like(frame_starts, dtype=float)
+        else:
+            frame_decay = np.asarray(decay_correction_factor, dtype=float)
+            if frame_decay.shape != frame_starts.shape:
+                raise ValueError("decay_correction_factor must have the same shape as frame_starts")
+
+        return cls(duration=frame_duration,
+                   start=frame_starts,
+                   end=frame_ends,
+                   center=frame_midpoint,
+                   decay=frame_decay)
+
 
 def get_window_index_pairs_from_durations(frame_durations: np.ndarray, w_size: float):
     r"""
@@ -263,25 +306,29 @@ def get_window_index_pairs_for_image(image_path: str, w_size: float):
                                                  w_size=w_size)
 
 
-def calculate_frame_reference_time(frame_duration: float,
-                                   frame_start: float,
-                                   half_life: float) -> float:
+def calculate_frame_reference_time(frame_duration: np.ndarray,
+                                   frame_start: np.ndarray,
+                                   half_life: float) -> np.ndarray:
     r"""Compute frame reference time as the time at which the average activity occurs.
     
-    Equation comes from the `DICOM standard documentation <https://dicom.innolitics.com/ciods/positron-emission-tomography-image/pet-image/00541300>`_
+    Equation comes from the `DICOM standard documentation
+    <https://dicom.innolitics.com/ciods/positron-emission-tomography-image/pet-image/00541300>`_
 
     :math:`T_{ave}=\frac{1}{\lambda}ln\frac{\lambda T}{1-e^{-\lambda T}}`
 
-    where lambda is the decay constant, :math:`\frac{ln2}{T_{1/2}}`, :math:`T_{1/2}` is the half life, and :math:`T` is the frame duration.
+    where lambda is the decay constant, :math:`\frac{ln2}{T_{1/2}}`, :math:`T_{1/2}` is the half
+    life, and :math:`T` is the frame duration.
 
     Args:
-        frame_duration (float): Frame Duration in seconds
-        frame_start (float): Start time of frame relative to scan start, in seconds
-        half_life (float): Radionuclide half life
+        frame_duration (np.ndarray): Duration of each frame in seconds.
+        frame_start (np.ndarray): Start time of each frame relative to scan start, in seconds.
+        half_life (float): Radionuclide half life in seconds.
 
     Returns: 
-        float: Frame reference time
+        np.ndarray: Frame reference time for each frame in the scan in seconds.
     """
-    decay_constant = math.log(2)/half_life
-    frame_reference_time = frame_start + math.log((decay_constant*frame_duration)/(1-math.exp(-decay_constant*frame_duration)))/decay_constant
+    decay_constant = np.log(2)/half_life
+    decay_over_frame = decay_constant*frame_duration
+    reference_time_delay = np.log((decay_over_frame)/(1-np.exp(-decay_over_frame)))/decay_constant
+    frame_reference_time = frame_start + reference_time_delay
     return frame_reference_time

{petpal-0.5.7.dist-info → petpal-0.5.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: petpal
-Version: 0.5.7
+Version: 0.5.8
 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-0.5.7.dist-info → petpal-0.5.8.dist-info}/RECORD

@@ -37,7 +37,7 @@ petpal/pipelines/preproc_steps.py,sha256=VC-KoMwxnfv0BxUEGneDjDy6HUYAub6JztaRHm3
 petpal/pipelines/steps_base.py,sha256=W7GVN5-tsXe_7fvhoMRIlOk5ggY8V2wpSSmDONphLnQ,18311
 petpal/pipelines/steps_containers.py,sha256=TV4LkPK48OnAds10vLcsPI3qtWjHsmwr6XGu3hup59Q,33767
 petpal/preproc/__init__.py,sha256=HmTVnCiKMxetDT_w-qU_62UOC39_A83LHXhZm07Q81I,504
-petpal/preproc/decay_correction.py,sha256=QCA_QcB6pqAD_wYSqtRKSvO6qWCaEzgL_qrAcSczRtw,6829
+petpal/preproc/decay_correction.py,sha256=jT8X2lmMrdGf9-lo1ooKul_yomPqm1p24gB9On_GHl0,6872
 petpal/preproc/image_operations_4d.py,sha256=IqzwxaWxoWC1gmK00uuHIwlhx8e_eQ44C6yVFuu73W4,31371
 petpal/preproc/motion_corr.py,sha256=dz10qjXBVTF_RH5RPZ68drUVX2qyj-MnZ674_Ccwz2Y,28670
 petpal/preproc/motion_target.py,sha256=_OJp3NoYcyD3Ke3wl2KbfOhbJ6dp6ZduR9LLz0rIaC0,3945
@@ -55,7 +55,7 @@ petpal/utils/decorators.py,sha256=9CVT4rXnSUqryNL83jmhQHiI6IGDr2E8jBqPD-KhYGA,49
 petpal/utils/image_io.py,sha256=2Dj2U-OaGL15lwt8KVyl_RZZZdRYdvzUahQWegO_JrA,17995
 petpal/utils/math_lib.py,sha256=DYt80lB1je-wFqHGuzOwfTOM1tPugomB889xBUdr99U,4725
 petpal/utils/metadata.py,sha256=O9exRDlqAmPAEcO9v7dsqzkYcSVLgRA207owEvNXXJ8,6129
-petpal/utils/scan_timing.py,sha256=j7i66Nt0Qs3fnQLUaycLHQTfVsNOqS7YS-xUJKm7nYk,11795
+petpal/utils/scan_timing.py,sha256=CYtYuFquAnOQ2QfjXdeLjWrBDPM_k4vBI9oHQdpmVZ0,13908
 petpal/utils/stats.py,sha256=paFdwVPIjlAi0wh5xU4x5WeydjKsEHuwzMLcDG_WzPc,6449
 petpal/utils/testing_utils.py,sha256=eMt1kklxK3rl8tm74I3yVNDotKh1CnYWLINDT7rzboM,9557
 petpal/utils/time_activity_curve.py,sha256=gX3PDYbeWblycvtvyiuFtnv1mBml_-93sIXKh2EmglM,39137
@@ -65,8 +65,8 @@ 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-0.5.7.dist-info/METADATA,sha256=9fNNCPhSznboKgTX9xPVDIDTJXquMiPoh66Bq-PN9lg,2617
-petpal-0.5.7.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-petpal-0.5.7.dist-info/entry_points.txt,sha256=0SZmyXqBxKzQg2eerDA16n2BdUEXyixEm0_AUo2dFns,653
-petpal-0.5.7.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-petpal-0.5.7.dist-info/RECORD,,
+petpal-0.5.8.dist-info/METADATA,sha256=p2q6Rl726zTvyMW39Uw3j4jw0dXYKFhIDvkGG9nXqKk,2617
+petpal-0.5.8.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+petpal-0.5.8.dist-info/entry_points.txt,sha256=0SZmyXqBxKzQg2eerDA16n2BdUEXyixEm0_AUo2dFns,653
+petpal-0.5.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+petpal-0.5.8.dist-info/RECORD,,