added a few flim convenience functions

Author: StephenThornquist

.github/workflows/ci.yml

@@ -32,6 +32,7 @@ jobs:
           CIBW_TEST_COMMAND: >
             cd {package} &&
             pytest tests
+          
           DROPBOX_SECRET: ${{ secrets.DROPBOX_SECRET }}
           DROPBOX_APP_KEY: ${{ secrets.DROPBOX_APP_KEY }}
           DROPBOX_REFRESH_TOKEN: ${{ secrets.DROPBOX_REFRESH_TOKEN }}

siffpy/core/flim/__init__.py

@@ -8,7 +8,7 @@
 from typing import Union
 from siffpy.core.flim.flimparams import FLIMParams, Exp, Irf # noqa: F401
 from siffpy.core.flim.multi_pulse import MultiPulseFLIMParams, MultiIrf, FractionalIrf # noqa: F401
-from siffpy.core.flim.flimunits import FlimUnits, convert_flimunits # noqa: F401
+from siffpy.core.flim.flimunits import FlimUnits, convert_flimunits, FlimUnitsLike # noqa: F401
 
 import numpy as np
 

siffpy/core/flim/flimparams.py

@@ -388,6 +388,21 @@ def T_O(self)->float:
         """ Back-compatibility """
         return self.tau_offset
 
+    @property
+    def offsets(self) -> List[Tuple[float, float]]:
+        """
+        All offsets in a list format paired with their
+        corresponding weights. For a single IRF, this is
+        a weight of 1, but if there are multiple laser pulses
+        the weights will sum to one.
+
+        # Returns
+
+        - `offsets : List[Tuple[float, float]]`
+            [(offset, weight), ...]
+        """
+        return [(self.tau_offset, 1)]
+    
     @property
     def noise(self)->float:
         """

siffpy/core/flim/multi_pulse.py

@@ -4,7 +4,7 @@
 """
 from typing import (
     Any, Union, List, Tuple, Dict, Optional,
-    TYPE_CHECKING, Callable
+    TYPE_CHECKING, Callable, Iterator,
 )
 
 import numpy as np
@@ -235,7 +235,7 @@ def __setitem__(self, index:int, value:FractionalIrf):
         """
         self.irfs[index] = value
 
-    def __iter__(self):
+    def __iter__(self) -> Iterator[FractionalIrf]:
         """
         Iterates over the IRFs
         """
@@ -270,6 +270,13 @@ def __init__(
                 arg for arg in args if isinstance(arg, MultiIrf)
             )
 
+    @property
+    def offsets(self) -> List[Tuple[float, float]]:
+        return [
+            (irf.tau_offset, irf.frac)
+            for irf in self.irfs
+        ]
+
     @property
     def irfs(self)->MultiIrf:
         """

siffpy/core/siffreader.py

@@ -7,7 +7,7 @@
 
 ## Should I move some import statements to function definitions
 from siffpy.core import io, timetools
-from siffpy.core.flim import FLIMParams, FlimUnits, default_flimparams
+from siffpy.core.flim import FLIMParams, FlimUnits, default_flimparams, FlimUnitsLike
 from siffpy.core.utils.event_stamp import EventStamp
 
 #from siffpy.core.utils import ImParams
@@ -1464,6 +1464,7 @@ def get_frames_flim(
         registration_dict : Optional[Dict] = None,
         confidence_metric : str = 'chi_sq',
         method : Union[str, FlimMethod] = FlimMethod.EMPIRICAL,
+        units : 'FlimUnitsLike' = 'nanoseconds',
         ) -> FlimTrace:
         """
         Returns a FlimTrace object of dimensions
@@ -1498,15 +1499,17 @@ def get_frames_flim(
             confidence_metric=confidence_metric
         )    
 
-        return FlimTrace(
+        ft = FlimTrace(
             lifetime,
             intensity = intensity,
             #confidence= np.array(flim_arrays[2]),
             FLIMParams = params,
             method = method.value,
-            units = 'countbins',
         )
 
+        ft.convert_units(units)
+        return ft
+
     def _get_frames_flim_srm(
         self,
         params : FLIMParams,
@@ -1574,6 +1577,7 @@ def sum_mask_flim(
         registration_dict : Optional[dict] = None,
         return_framewise : bool = False,
         flim_method : Union[str, FlimMethod] = FlimMethod.EMPIRICAL,
+        units : 'FlimUnitsLike' = 'nanoseconds',
         )->FlimTrace:
         """
         Computes the empirical lifetime within an ROI over timesteps.
@@ -1621,6 +1625,9 @@ def sum_mask_flim(
         * `flim_method` : Union[str, FlimMethod]
             The method to use for the FLIM analysis. Default is 'empirical'.
             Options are any of the `FlimMethod` enum values (`siffpy.siffmath.flim.FlimMethod`).
+
+        * `units` : FlimUnitsLike
+            The units to return the FLIM data in. Default is 'nanoseconds'.
             
         # Returns
 
@@ -1689,7 +1696,7 @@ def sum_mask_flim(
         )
 
         if return_framewise:
-            return FlimTrace(
+            ft = FlimTrace(
                 summed_flim_data, 
                 intensity = summed_intensity_data,
                 FLIMParams = params,
@@ -1698,7 +1705,10 @@ def sum_mask_flim(
                 units = FlimUnits.COUNTBINS,
             )
 
-        return FlimTrace(
+            ft.convert_units(units)
+            return ft
+
+        ft = FlimTrace(
             summed_flim_data, 
             intensity = summed_intensity_data,
             FLIMParams = params,
@@ -1708,6 +1718,9 @@ def sum_mask_flim(
         ).reshape(
             (-1, mask.shape[0] if mask.ndim > 2 else 1)
         ).sum(axis=1)
+
+        ft.convert_units(units)
+        return ft
 
     def _sum_mask_flim_srm(
         self,
@@ -1816,6 +1829,7 @@ def sum_masks_flim(
         registration_dict : Optional[dict] = None,
         return_framewise : bool = False,
         flim_method : Union[str, FlimMethod] = FlimMethod.EMPIRICAL,
+        units : 'FlimUnitsLike' = 'nanoseconds',
         )->FlimTrace:
         """
         Computes the empirical lifetime within a set of ROIs over timesteps.
@@ -1852,6 +1866,9 @@ def sum_masks_flim(
         * `flim_method` : Union[str, FlimMethod]
             The method to use for the FLIM analysis. Default is 'empirical'.
             Options are any of the `FlimMethod` enum values (`siffpy.siffmath.flim.FlimMethod`).
+
+        * `units` : FlimUnitsLike
+            The units to return the FLIM data in. Default is 'nanoseconds'.
         
         # Returns
 
@@ -1930,7 +1947,7 @@ def sum_masks_flim(
         )
 
         if return_framewise:
-            return FlimTrace(
+            ft = FlimTrace(
                 flim_summed,
                 intensity = intensity_summed,
                 FLIMParams = params,
@@ -1939,9 +1956,12 @@ def sum_masks_flim(
                 units = FlimUnits.COUNTBINS,
             )
 
+            ft.convert_units(units)
+            return ft
+
         # Reshape AFTER making a `FlimTrace`
         # or else things won't be added correctly.
-        return FlimTrace(
+        ft = FlimTrace(
             flim_summed,
             intensity = intensity_summed,
             FLIMParams = params,
@@ -1952,8 +1972,9 @@ def sum_masks_flim(
             (masks.shape[0], -1, masks.shape[1] if masks.ndim > 3 else 1)
         ).sum(axis=2)
 
-        raise NotImplementedError("Not yet implemented using corrosiff backend")
-    
+        ft = ft.convert_units(units)
+        return ft
+
     def _sum_masks_flim_srm(
         self,
         params : FLIMParams,