cq: update warnings with automatic stack_level

lumicks/pylake/detail/confocal.py

@@ -8,7 +8,7 @@
 
 from .image import reconstruct_image, reconstruct_image_sum
 from .mixin import PhotonCounts, ExcitationLaserPower
-from .utilities import method_cache, could_sum_overflow
+from .utilities import method_cache, find_stack_level, could_sum_overflow
 from ..adjustments import no_adjustment
 from .imaging_mixins import TiffExport
 
@@ -348,7 +348,8 @@ def _tiff_image_metadata(self) -> dict:
         except NotImplementedError:
             warnings.warn(
                 f"Pixel times are not defined for this {self.__class__.__name__}. "
-                "The corresponding metadata in the output file is set to `None`."
+                "The corresponding metadata in the output file is set to `None`.",
+                stacklevel=find_stack_level(),
             )
             pixel_time_seconds = None
 

lumicks/pylake/detail/image.py

@@ -4,6 +4,8 @@
 
 import numpy as np
 
+from .utilities import find_stack_level
+
 
 class InfowaveCode(enum.IntEnum):
     discard = 0  # this data sample does not contain useful information
@@ -195,7 +197,9 @@ def histogram_rows(image, pixels_per_bin, pixel_width):
     remainder = n_rows % pixels_per_bin
     if remainder != 0:
         warnings.warn(
-            f"{n_rows} pixels is not divisible by {pixels_per_bin}, final bin only contains {remainder} pixels"
+            f"{n_rows} pixels is not divisible by {pixels_per_bin}, final bin only contains "
+            f"{remainder} pixels",
+            stacklevel=find_stack_level(),
         )
         pad = np.zeros((pixels_per_bin - remainder, image.shape[1]))
         image = np.vstack((image, pad))

lumicks/pylake/detail/utilities.py

@@ -1,7 +1,7 @@
 import math
-import contextlib
-import pathlib
 import inspect
+import pathlib
+import contextlib
 
 import numpy as np
 import cachetools

lumicks/pylake/detail/widefield.py

@@ -8,6 +8,7 @@
 import numpy as np
 import tifffile
 
+from .utilities import find_stack_level
 from ..adjustments import no_adjustment
 
 
@@ -161,7 +162,7 @@ def __init__(self, tiff_files, align_requested, roi=None, tether=None):
         # warn on file open if alignment is requested, but not possible
         # stacklevel=4 corresponds to ImageStack.__init__()
         if self._description._alignment.has_problem:
-            warnings.warn(self._description._alignment.status.value, stacklevel=4)
+            warnings.warn(self._description._alignment.status.value, stacklevel=find_stack_level())
 
         if roi is None:
             self._roi = Roi(0, self._description.width, 0, self._description.height)

lumicks/pylake/file.py

@@ -14,6 +14,7 @@
 from .calibration import ForceCalibration
 from .detail.mixin import Force, PhotonCounts, DownsampledFD, PhotonTimeTags, BaselineCorrectedForce
 from .detail.h5_helper import write_h5
+from .detail.utilities import find_stack_level
 
 __all__ = ["File"]
 
@@ -262,7 +263,7 @@ def try_from_dataset(*args):
             try:
                 return cls.from_dataset(*args)
             except Exception as e:
-                warnings.warn(e.args[0])
+                warnings.warn(e.args[0], stacklevel=find_stack_level())
                 return None
 
         if field not in self.h5:

lumicks/pylake/fitting/detail/derivative_manipulation.py

@@ -3,6 +3,8 @@
 import numpy as np
 import scipy
 
+from ...detail.utilities import find_stack_level
+
 
 def numerical_diff(fn, x, dx=1e-6):
     return (fn(x + dx) - fn(x - dx)) / (2.0 * dx)
@@ -126,7 +128,8 @@ def invert_function_interpolation(
         except Exception as e:
             warnings.warn(
                 f"Interpolation failed. Cause: {e}. Falling back to brute force evaluation. "
-                f"Results should be fine, but slower."
+                f"Results should be fine, but slower.",
+                stacklevel=find_stack_level(),
             )
             result[interpolated_idx] = manual_inversion(d[interpolated_idx], initial)
     else:

lumicks/pylake/fitting/detail/model_implementation.py

@@ -4,6 +4,7 @@
 
 from .utilities import latex_frac, latex_sqrt, solve_formatter, solve_formatter_tex
 from ..parameters import Parameter
+from ...detail.utilities import find_stack_level
 from .derivative_manipulation import invert_function, invert_jacobian, invert_function_interpolation
 
 
@@ -103,8 +104,10 @@ def wlc_marko_siggia_force(d, Lp, Lc, kT):
 
     if np.any(d > Lc):
         warnings.warn(
-            "Marko Siggia model is only defined properly up to the contour length (d = Lc)",
-            RuntimeWarning,
+            RuntimeWarning(
+                "Marko Siggia model is only defined properly up to the contour length (d = Lc)"
+            ),
+            stacklevel=find_stack_level(),
         )
 
     d_div_Lc = d / Lc

lumicks/pylake/force_calibration/power_spectrum.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-from lumicks.pylake.detail.utilities import downsample
+from lumicks.pylake.detail.utilities import downsample, find_stack_level
 
 
 class PowerSpectrum:
@@ -52,7 +52,10 @@ def squared_fft(d):
             int(np.round(window_seconds * sample_rate)) if window_seconds else len(data)
         )
         if num_points_per_window > len(data):
-            warnings.warn(RuntimeWarning("Longer window than data duration: not using windowing."))
+            warnings.warn(
+                RuntimeWarning("Longer window than data duration: not using windowing."),
+                stacklevel=find_stack_level(),
+            )
             num_points_per_window = len(data)
 
         squared_fft_chunks = [

lumicks/pylake/force_calibration/touchdown.py

@@ -4,7 +4,7 @@
 import numpy as np
 import scipy
 
-from lumicks.pylake.detail.utilities import downsample
+from lumicks.pylake.detail.utilities import downsample, find_stack_level
 
 
 def mack_model(
@@ -82,7 +82,8 @@ def f_test(sse_restricted, sse_unrestricted, num_data, num_pars_difference, num_
             RuntimeWarning(
                 "Denominator in F-Test is zero. "
                 "This may be caused by using noise-free data or fewer than 4 data points."
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
         return 0.0
     else:
@@ -310,15 +311,17 @@ def touchdown(
             RuntimeWarning(
                 "Insufficient data available to reliably fit touchdown curve. We need at least two "
                 "oscillations to reliably fit the interference pattern."
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
         focal_shift = None
 
     if p_value > maximum_p_value:
         warnings.warn(
             RuntimeWarning(
                 "Surface detection failed (piecewise linear fit not better than linear fit)"
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
         surface_position = None
 

lumicks/pylake/group.py

@@ -1,6 +1,7 @@
 import warnings
 
 from .channel import channel_class
+from .detail.utilities import find_stack_level
 
 
 class Group:
@@ -34,9 +35,11 @@ def __getitem__(self, item):
         redirect_location, redirect_class = self._lk_file.redirect_list.get(item_type, (None, None))
         if redirect_location and not redirect_class:
             warnings.warn(
-                f"Direct access to this field is deprecated. Use file.{redirect_location} "
-                "instead. In case raw access is needed, go through the fn.h5 directly.",
-                FutureWarning,
+                FutureWarning(
+                    f"Direct access to this field is deprecated. Use file.{redirect_location} "
+                    "instead. In case raw access is needed, go through the fn.h5 directly.",
+                ),
+                stacklevel=find_stack_level(),
             )
 
         if type(thing) is h5py.Group:

lumicks/pylake/kymo.py

@@ -15,7 +15,7 @@
 from .detail.confocal import ScanAxis, ScanMetaData, ConfocalImage
 from .detail.plotting import get_axes, show_image
 from .detail.timeindex import to_timestamp
-from .detail.utilities import method_cache
+from .detail.utilities import method_cache, find_stack_level
 
 
 def _default_line_time_factory(self: "Kymo"):
@@ -292,8 +292,10 @@ def _fix_incorrect_start(self):
         self.start = seek_timestamp_next_line(self.infowave[self.start :])
         self._cache = {}
         warnings.warn(
-            "Start of the kymograph was truncated. Omitting the truncated first line.",
-            RuntimeWarning,
+            RuntimeWarning(
+                "Start of the kymograph was truncated. Omitting the truncated first line."
+            ),
+            stacklevel=find_stack_level(),
         )
 
     def _to_spatial(self, data):
@@ -488,7 +490,10 @@ def set_aspect_ratio(axis, ar):
                 )
 
             warnings.warn(
-                RuntimeWarning("Using downsampled force since high frequency force is unavailable.")
+                RuntimeWarning(
+                    "Using downsampled force since high frequency force is unavailable."
+                ),
+                stacklevel=find_stack_level(),
             )
 
         time_ranges = self.line_timestamp_ranges(include_dead_time=False)

lumicks/pylake/kymotracker/detail/msd_estimation.py

@@ -5,6 +5,8 @@
 import numpy as np
 import numpy.typing as npt
 
+from ...detail.utilities import find_stack_level
+
 
 @dataclass(frozen=True)
 class DiffusionEstimate:
@@ -472,7 +474,10 @@ def _diffusion_gls(lag_idx, mean_squared_displacements, num_points, tolerance=1e
 
     def fallback(warning_message):
         """Fallback method if the GLS fails"""
-        warnings.warn(RuntimeWarning(f"{warning_message} Reverting to two-point OLS."))
+        warnings.warn(
+            RuntimeWarning(f"{warning_message} Reverting to two-point OLS."),
+            stacklevel=find_stack_level(),
+        )
         return _diffusion_ols(lag_idx[:2], mean_squared_displacements[:2], num_points)
 
     # Since the covariance matrix depends on the parameters for the intercept and slope, we obtain
@@ -600,7 +605,7 @@ def estimate_diffusion_constant_simple(
                     "`help(lk.refine_tracks_centroid)` or `help(lk.refine_tracks_gaussian)` for "
                     "more information."
                 ),
-                stacklevel=2,
+                stacklevel=find_stack_level(),
             )
 
     frame_lags, msd = calculate_msd(frame_idx, coordinate, max_lag)
@@ -718,7 +723,8 @@ def determine_optimal_points(frame_idx, coordinate, max_iterations=100):
             RuntimeWarning(
                 "Your tracks have missing frames. Note that this can lead to a suboptimal "
                 "estimate of the optimal number of lags when using OLS."
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
 
     num_slope = max(2, len(coordinate) // 10)  # Need at least two points for a linear regression!
@@ -744,7 +750,8 @@ def determine_optimal_points(frame_idx, coordinate, max_iterations=100):
             return num_slope, num_intercept
 
     warnings.warn(
-        RuntimeWarning("Warning, maximum number of iterations exceeded. Returning best solution.")
+        RuntimeWarning("Warning, maximum number of iterations exceeded. Returning best solution."),
+        stacklevel=find_stack_level(),
     )
     return num_slope, num_intercept
 
@@ -1123,7 +1130,8 @@ def _determine_optimal_points_ensemble(frame_lags, msds, n_coord, max_iterations
             return num_slope
 
     warnings.warn(
-        RuntimeWarning("Warning, maximum number of iterations exceeded. Returning best solution.")
+        RuntimeWarning("Warning, maximum number of iterations exceeded. Returning best solution."),
+        stacklevel=find_stack_level(),
     )
 
     return num_slope
@@ -1137,7 +1145,8 @@ def ensemble_ols(kymotracks, max_lag):
         warnings.warn(
             RuntimeWarning(
                 "Your tracks have missing frames. Note that this can lead to a suboptimal estimates"
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
 
     optimal_lags = (

lumicks/pylake/kymotracker/kymotrack.py

@@ -4,7 +4,7 @@
 from copy import copy
 
 from ..__about__ import __version__
-from ..detail.utilities import replace_key_aliases
+from ..detail.utilities import find_stack_level, replace_key_aliases
 from .detail.peakfinding import _sum_track_signal
 from ..population.dwelltime import DwelltimeModel
 from .detail.msd_estimation import *
@@ -191,7 +191,7 @@ def import_kymotrackgroup_from_csv(filename, kymo, channel, delimiter=";"):
                     "File contains non-integer time indices; round-off errors may have occurred "
                     "when loading the data"
                 ),
-                stacklevel=2,
+                stacklevel=find_stack_level(),
             )
 
     def create_track(time, coord, min_length=None):
@@ -553,7 +553,7 @@ def sample_from_image(self, num_pixels, reduce=np.sum, *, correct_origin=None):
                     "ensure backward compatibility. To silence this warning use "
                     "`correct_origin=False`."
                 ),
-                stacklevel=2,
+                stacklevel=find_stack_level(),
             )
 
         # Time and coordinates are being cast to an integer since we use them to index into a data
@@ -866,7 +866,8 @@ def estimate_diffusion(
                     RuntimeWarning(
                         "Motion blur cannot be taken into account for this type of Kymo. As a "
                         "consequence, not all estimates will be available."
-                    )
+                    ),
+                    stacklevel=find_stack_level(),
                 )
                 blur = np.nan
 
@@ -1579,7 +1580,8 @@ def fit_binding_times(
                     "warning, but use the deprecated behavior use `observed_minimum=True`. To "
                     "enable the recommended method of estimating the minimum observable dwell "
                     "time use `observed_minimum=False`."
-                )
+                ),
+                stacklevel=find_stack_level(),
             )
             observed_minimum = True
 
@@ -1594,7 +1596,8 @@ def fit_binding_times(
                     "version of Pylake (`2.0.0`), using the discrete model will become the "
                     "default. Until then, the continuous model is still used for backward "
                     "compatibility."
-                )
+                ),
+                stacklevel=find_stack_level(),
             )
             discrete_model = False
 
@@ -1623,7 +1626,7 @@ def fit_binding_times(
                     "dropped from the analysis. If you wish to not see this warning, filter the "
                     "tracks with `lk.filter_tracks` with a minimum length of 2 samples."
                 ),
-                stacklevel=2,
+                stacklevel=find_stack_level(),
             )
 
         if dwelltimes.size == 0:
@@ -1807,10 +1810,11 @@ def estimate_diffusion(self, method, *args, min_length=None, **kwargs):
 
         if n_discarded and min_length is None:
             warnings.warn(
-                f"{n_discarded} tracks were shorter than the specified min_length "
-                "and discarded from the analysis.",
-                RuntimeWarning,
-                stacklevel=2,
+                RuntimeWarning(
+                    f"{n_discarded} tracks were shorter than the specified min_length and "
+                    f"discarded from the analysis.",
+                ),
+                stacklevel=find_stack_level(),
             )
 
         return [k.estimate_diffusion(method, *args, **kwargs) for k in filtered_tracks]
@@ -1871,6 +1875,7 @@ def ensemble_diffusion(self, method, *, max_lag=None):
                         "Localization variances cannot be reliably calculated for an ensemble of "
                         "tracks from kymographs with different line times or pixel sizes."
                     ),
+                    stacklevel=find_stack_level(),
                 )
                 is_valid = False
             return ensemble_cve(self, calculate_localization_var=is_valid)