From 97479d4bc4ddb118b121a1eb0c7af04edaaab76c Mon Sep 17 00:00:00 2001
From: JoepVanlier <joep.vanlier@gmail.com>
Date: Fri, 4 Aug 2023 14:39:04 +0200
Subject: [PATCH] cq: update warnings with automatic stack_level

---
 lumicks/pylake/detail/confocal.py             |  5 ++--
 lumicks/pylake/detail/image.py                |  6 ++++-
 lumicks/pylake/detail/utilities.py            |  4 +--
 lumicks/pylake/detail/widefield.py            |  3 ++-
 lumicks/pylake/file.py                        |  3 ++-
 .../fitting/detail/derivative_manipulation.py |  5 +++-
 .../fitting/detail/model_implementation.py    |  7 +++--
 .../force_calibration/power_spectrum.py       |  7 +++--
 lumicks/pylake/force_calibration/touchdown.py | 11 +++++---
 lumicks/pylake/group.py                       |  9 ++++---
 lumicks/pylake/kymo.py                        | 13 ++++++---
 .../kymotracker/detail/msd_estimation.py      | 21 ++++++++++-----
 lumicks/pylake/kymotracker/kymotrack.py       | 27 +++++++++++--------
 lumicks/pylake/kymotracker/kymotracker.py     |  9 +++++--
 lumicks/pylake/nb_widgets/correlated_plot.py  |  7 ++++-
 .../pylake/nb_widgets/kymotracker_widgets.py  |  5 +++-
 .../pylake/piezo_tracking/piezo_tracking.py   |  4 ++-
 17 files changed, 101 insertions(+), 45 deletions(-)

diff --git a/lumicks/pylake/detail/confocal.py b/lumicks/pylake/detail/confocal.py
index 3fe9e646c..e9e3424f1 100644
--- a/lumicks/pylake/detail/confocal.py
+++ b/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
 
diff --git a/lumicks/pylake/detail/image.py b/lumicks/pylake/detail/image.py
index dcd3a4b32..0e2517025 100644
--- a/lumicks/pylake/detail/image.py
+++ b/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))
diff --git a/lumicks/pylake/detail/utilities.py b/lumicks/pylake/detail/utilities.py
index 5efd0b03b..7523f28a6 100644
--- a/lumicks/pylake/detail/utilities.py
+++ b/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
diff --git a/lumicks/pylake/detail/widefield.py b/lumicks/pylake/detail/widefield.py
index 2ad76d75b..3dca6d5b2 100644
--- a/lumicks/pylake/detail/widefield.py
+++ b/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)
diff --git a/lumicks/pylake/file.py b/lumicks/pylake/file.py
index 8e6e9f3b1..308b9a308 100644
--- a/lumicks/pylake/file.py
+++ b/lumicks/pylake/file.py
@@ -15,6 +15,7 @@
 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"]
 
@@ -260,7 +261,7 @@ 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:
diff --git a/lumicks/pylake/fitting/detail/derivative_manipulation.py b/lumicks/pylake/fitting/detail/derivative_manipulation.py
index 630847d1c..fade8af2b 100644
--- a/lumicks/pylake/fitting/detail/derivative_manipulation.py
+++ b/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:
diff --git a/lumicks/pylake/fitting/detail/model_implementation.py b/lumicks/pylake/fitting/detail/model_implementation.py
index a6b33566c..4b63be3d0 100644
--- a/lumicks/pylake/fitting/detail/model_implementation.py
+++ b/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
diff --git a/lumicks/pylake/force_calibration/power_spectrum.py b/lumicks/pylake/force_calibration/power_spectrum.py
index 637a4e4a4..4cde3c0de 100644
--- a/lumicks/pylake/force_calibration/power_spectrum.py
+++ b/lumicks/pylake/force_calibration/power_spectrum.py
@@ -5,7 +5,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from lumicks.pylake.detail.utilities import downsample
+from lumicks.pylake.detail.utilities import downsample, find_stack_level
 
 
 class PowerSpectrum:
@@ -53,7 +53,10 @@ 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 = [
diff --git a/lumicks/pylake/force_calibration/touchdown.py b/lumicks/pylake/force_calibration/touchdown.py
index 041d0daa7..d9f8bcb80 100644
--- a/lumicks/pylake/force_calibration/touchdown.py
+++ b/lumicks/pylake/force_calibration/touchdown.py
@@ -5,7 +5,7 @@
 import scipy
 import matplotlib.pyplot as plt
 
-from lumicks.pylake.detail.utilities import downsample
+from lumicks.pylake.detail.utilities import downsample, find_stack_level
 
 
 def mack_model(
@@ -83,7 +83,8 @@ 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:
@@ -309,7 +310,8 @@ 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
 
@@ -317,7 +319,8 @@ def touchdown(
         warnings.warn(
             RuntimeWarning(
                 "Surface detection failed (piecewise linear fit not better than linear fit)"
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
         surface_position = None
 
diff --git a/lumicks/pylake/group.py b/lumicks/pylake/group.py
index 5d7f00e6f..a61921fc2 100644
--- a/lumicks/pylake/group.py
+++ b/lumicks/pylake/group.py
@@ -3,6 +3,7 @@
 import h5py
 
 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:
diff --git a/lumicks/pylake/kymo.py b/lumicks/pylake/kymo.py
index 58921b26e..3b77fd94b 100644
--- a/lumicks/pylake/kymo.py
+++ b/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)
diff --git a/lumicks/pylake/kymotracker/detail/msd_estimation.py b/lumicks/pylake/kymotracker/detail/msd_estimation.py
index 38ff4b637..1ecdd5027 100644
--- a/lumicks/pylake/kymotracker/detail/msd_estimation.py
+++ b/lumicks/pylake/kymotracker/detail/msd_estimation.py
@@ -6,6 +6,8 @@
 import numpy.typing as npt
 import matplotlib.pyplot as plt
 
+from ...detail.utilities import find_stack_level
+
 
 @dataclass(frozen=True)
 class DiffusionEstimate:
@@ -471,7 +473,10 @@ 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
@@ -599,7 +604,7 @@ 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)
@@ -717,7 +722,8 @@ 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!
@@ -743,7 +749,8 @@ 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
 
@@ -1122,7 +1129,8 @@ 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
@@ -1136,7 +1144,8 @@ 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 = (
diff --git a/lumicks/pylake/kymotracker/kymotrack.py b/lumicks/pylake/kymotracker/kymotrack.py
index 60a72069c..c8bab17fd 100644
--- a/lumicks/pylake/kymotracker/kymotrack.py
+++ b/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):
@@ -551,7 +551,7 @@ 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
@@ -863,7 +863,8 @@ 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
 
@@ -1574,7 +1575,8 @@ 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
 
@@ -1589,7 +1591,8 @@ 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."
-                )
+                ),
+                stack_level=find_stack_level(),
             )
             discrete_model = False
 
@@ -1618,7 +1621,7 @@ 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:
@@ -1802,10 +1805,11 @@ 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]
@@ -1866,6 +1870,7 @@ 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)
diff --git a/lumicks/pylake/kymotracker/kymotracker.py b/lumicks/pylake/kymotracker/kymotracker.py
index 0e8953431..0f1c689c9 100644
--- a/lumicks/pylake/kymotracker/kymotracker.py
+++ b/lumicks/pylake/kymotracker/kymotracker.py
@@ -4,6 +4,7 @@
 import numpy as np
 
 from .kymotrack import KymoTrack, KymoTrackGroup
+from ..detail.utilities import find_stack_level
 from .detail.peakfinding import (
     KymoPeaks,
     peak_estimate,
@@ -561,7 +562,8 @@ def refine_tracks_gaussian(
                 "track when a track momentarily disappears. When using the overlap strategy "
                 '"multiple" individual overlapping Gaussians could switch positions leading to'
                 "spurious track crossings."
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
 
     if len(tracks._kymos) > 1:
@@ -647,7 +649,10 @@ def refine_tracks_gaussian(
 
     if overlap_count and overlap_strategy != "ignore":
         warnings.warn(
-            f"There were {overlap_count} instances of overlapped tracks ignored while fitting."
+            UserWarning(
+                f"There were {overlap_count} instances of overlapped tracks ignored while fitting."
+            ),
+            stacklevel=find_stack_level(),
         )
 
     return KymoTrackGroup(
diff --git a/lumicks/pylake/nb_widgets/correlated_plot.py b/lumicks/pylake/nb_widgets/correlated_plot.py
index db46e8b42..727129217 100644
--- a/lumicks/pylake/nb_widgets/correlated_plot.py
+++ b/lumicks/pylake/nb_widgets/correlated_plot.py
@@ -2,6 +2,8 @@
 
 import numpy as np
 
+from ..detail.utilities import find_stack_level
+
 
 def plot_correlated(
     channel_slice,
@@ -46,7 +48,10 @@ def plot_correlated(
     downsampled = channel_slice.downsampled_over(frame_timestamps, where="left", reduce=reduce)
 
     if len(downsampled.timestamps) < len(frame_timestamps):
-        warnings.warn("Only subset of time range available for selected channel")
+        warnings.warn(
+            UserWarning("Only subset of time range available for selected channel"),
+            stacklevel=find_stack_level(),
+        )
 
     plot_data = get_plot_data(frame)
     aspect_ratio = plot_data.shape[0] / np.max([plot_data.shape])
diff --git a/lumicks/pylake/nb_widgets/kymotracker_widgets.py b/lumicks/pylake/nb_widgets/kymotracker_widgets.py
index 5aaf3c189..f5a7c1792 100644
--- a/lumicks/pylake/nb_widgets/kymotracker_widgets.py
+++ b/lumicks/pylake/nb_widgets/kymotracker_widgets.py
@@ -14,6 +14,8 @@
 from lumicks.pylake.nb_widgets.detail.mouse import MouseDragCallback
 from lumicks.pylake.nb_widgets.detail.undostack import UndoStack
 
+from ..detail.utilities import find_stack_level
+
 
 class KymoWidget:
     def __init__(
@@ -345,7 +347,8 @@ def save_tracks(self, filename, delimiter=";", sampling_width=None):
                     "when opening the kymotracking widget. The old (incorrect) behavior is "
                     "maintained until the next major release to ensure backward compatibility. "
                     "To silence this warning use `correct_origin=False`."
-                )
+                ),
+                stacklevel=find_stack_level(),
             )
             self._set_label(
                 "warning",
diff --git a/lumicks/pylake/piezo_tracking/piezo_tracking.py b/lumicks/pylake/piezo_tracking/piezo_tracking.py
index 0da386d12..ebc2fbf5c 100644
--- a/lumicks/pylake/piezo_tracking/piezo_tracking.py
+++ b/lumicks/pylake/piezo_tracking/piezo_tracking.py
@@ -5,6 +5,7 @@
 
 from ..channel import Slice
 from .baseline import ForceBaseLine
+from ..detail.utilities import find_stack_level
 
 __all__ = ["DistanceCalibration", "PiezoTrackingCalibration", "PiezoForceDistance"]
 
@@ -35,7 +36,8 @@ def __init__(self, trap_position, camera_distance, degree=1):
                 RuntimeWarning(
                     "There were frames with missing video tracking: "
                     f"{missed_frames} data point(s) were omitted."
-                )
+                ),
+                find_stack_level(),
             )
 
         coeffs = np.polyfit(self.position, self.distance, degree)