From d07c9ebc1e811124e8cf0676cf9860abc81fe2eb Mon Sep 17 00:00:00 2001
From: Tobias Jachowski <t.jachowski@lumicks.com>
Date: Mon, 8 May 2023 10:25:31 +0200
Subject: [PATCH 1/3] flake8: B028 got renamed to B907. See
 https://github.com/PyCQA/flake8-bugbear/pull/333

---
 .flake8 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.flake8 b/.flake8
index 84d9a80cd..13e7fc933 100644
--- a/.flake8
+++ b/.flake8
@@ -29,6 +29,6 @@ ignore =
     F403,F405,
     # Don't complain about f"'{x}'" quotes. `!r` is not particularly readable, especially not for
     # cases where one would have to resort to f"{str(x)!r}"
-    B028,
+    B907,
 
 show-source = True

From bc39954f7fb27323ca25168c984d5223de89aa83 Mon Sep 17 00:00:00 2001
From: JoepVanlier <joep.vanlier@gmail.com>
Date: Fri, 4 Aug 2023 14:39:21 +0200
Subject: [PATCH 2/3] qc: add a utility function for finding stack level

---
 lumicks/pylake/detail/utilities.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/lumicks/pylake/detail/utilities.py b/lumicks/pylake/detail/utilities.py
index 5816a7dcb..04a1be4b2 100644
--- a/lumicks/pylake/detail/utilities.py
+++ b/lumicks/pylake/detail/utilities.py
@@ -1,5 +1,7 @@
 import math
 import contextlib
+import pathlib
+import inspect
 
 import numpy as np
 import cachetools
@@ -213,3 +215,22 @@ def temp_seed(seed):
         yield
     finally:
         np.random.seed(None)
+
+
+def find_stack_level() -> int:
+    """Find where we leave the module"""
+    import lumicks.pylake as lk
+
+    pylake_folder = pathlib.Path(lk.__file__).parent
+
+    depth = 0
+    frame = inspect.currentframe()
+    while frame:
+        current_path = pathlib.Path(inspect.getfile(frame))
+        if pylake_folder in current_path.parents and "tests" not in current_path.parts:
+            frame = frame.f_back
+            depth += 1
+        else:
+            break
+
+    return depth

From ea89a78f0cf70fa45fc5800513972fe684511dc3 Mon Sep 17 00:00:00 2001
From: JoepVanlier <joep.vanlier@gmail.com>
Date: Fri, 4 Aug 2023 14:39:04 +0200
Subject: [PATCH 3/3] cq: update warnings with automatic stack_level

---
 lumicks/pylake/detail/confocal.py             |  5 +--
 lumicks/pylake/detail/image.py                |  6 +++-
 lumicks/pylake/detail/plotting.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/image_stack.py                 |  4 ++-
 lumicks/pylake/kymo.py                        | 13 +++++---
 .../kymotracker/detail/msd_estimation.py      | 21 ++++++++----
 lumicks/pylake/kymotracker/kymotrack.py       | 33 +++++++++++--------
 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 ++-
 lumicks/pylake/population/detail/hmm.py       |  8 +++--
 20 files changed, 118 insertions(+), 52 deletions(-)

diff --git a/lumicks/pylake/detail/confocal.py b/lumicks/pylake/detail/confocal.py
index 0c2916085..bbe1e414a 100644
--- a/lumicks/pylake/detail/confocal.py
+++ b/lumicks/pylake/detail/confocal.py
@@ -9,7 +9,7 @@
 from .image import reconstruct_image, reconstruct_image_sum
 from .mixin import PhotonCounts, ExcitationLaserPower
 from .plotting import parse_color_channel
-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
 
@@ -350,7 +350,8 @@ 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 247339921..c7bec5487 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
@@ -197,7 +199,9 @@ 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/plotting.py b/lumicks/pylake/detail/plotting.py
index 8f519b121..26b228bd1 100644
--- a/lumicks/pylake/detail/plotting.py
+++ b/lumicks/pylake/detail/plotting.py
@@ -1,6 +1,7 @@
 import warnings
 
 from ..adjustments import no_adjustment
+from ..detail.utilities import find_stack_level
 
 
 def get_axes(axes=None, image_handle=None):
@@ -36,8 +37,9 @@ def parse_color_channel(channel):
         warnings.warn(
             DeprecationWarning(
                 "In future versions, the `channel` argument will be restricted to lowercase "
-                f"letters only. Use '{channel}' instead of '{input_channel}'."
-            )
+                f"letters only. Use '{channel}' instead of '{input_channel}'.",
+            ),
+            stacklevel=find_stack_level(),
         )
 
     # check rgb order
diff --git a/lumicks/pylake/detail/utilities.py b/lumicks/pylake/detail/utilities.py
index 04a1be4b2..516b355cd 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 60539514d..3d324120b 100644
--- a/lumicks/pylake/detail/widefield.py
+++ b/lumicks/pylake/detail/widefield.py
@@ -9,6 +9,7 @@
 import tifffile
 
 from .plotting import parse_color_channel
+from .utilities import find_stack_level
 from ..adjustments import no_adjustment
 
 
@@ -205,7 +206,7 @@ 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 58e9ecf3e..f9f35a072 100644
--- a/lumicks/pylake/file.py
+++ b/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"]
 
@@ -276,7 +277,7 @@ 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 f776bb75c..194810ea3 100644
--- a/lumicks/pylake/force_calibration/power_spectrum.py
+++ b/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 = [
diff --git a/lumicks/pylake/force_calibration/touchdown.py b/lumicks/pylake/force_calibration/touchdown.py
index 6e1808636..a18a921bd 100644
--- a/lumicks/pylake/force_calibration/touchdown.py
+++ b/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:
@@ -310,7 +311,8 @@ 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
 
@@ -318,7 +320,8 @@ 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 65c0f289b..d0cf9479c 100644
--- a/lumicks/pylake/group.py
+++ b/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:
diff --git a/lumicks/pylake/image_stack.py b/lumicks/pylake/image_stack.py
index 8fc80a559..aab1f70d6 100644
--- a/lumicks/pylake/image_stack.py
+++ b/lumicks/pylake/image_stack.py
@@ -10,6 +10,7 @@
 from .adjustments import no_adjustment
 from .detail.image import make_image_title
 from .detail.plotting import get_axes, show_image
+from .detail.utilities import find_stack_level
 from .detail.widefield import TiffStack, _frame_timestamps_from_exposure_timestamps
 from .detail.imaging_mixins import FrameIndex, TiffExport, VideoExport
 
@@ -658,7 +659,8 @@ def frame_timestamp_ranges(self, *, include_dead_time=False):
                     "lag behind. This means that when you average data over the frame, some frames "
                     "after the switch may take an incorrect exposure time into account in the "
                     "averaging."
-                )
+                ),
+                stacklevel=find_stack_level(),
             )
 
         return frame_timestamps
diff --git a/lumicks/pylake/kymo.py b/lumicks/pylake/kymo.py
index f1d10014a..daddb75c6 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
 from .detail.bead_cropping import find_beads_template, find_beads_brightness
 
 
@@ -279,8 +279,10 @@ 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):
@@ -475,7 +477,10 @@ 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 370a63e8e..4003c99af 100644
--- a/lumicks/pylake/kymotracker/detail/msd_estimation.py
+++ b/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!
@@ -750,7 +756,8 @@ 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
 
@@ -1129,7 +1136,8 @@ 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
@@ -1143,7 +1151,8 @@ 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 5522c72f9..e774c9e74 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 *
@@ -154,7 +154,8 @@ def store_column(column_title, format_string, new_data):
                 "greater or equal to the minimum length used for the original tracking. For more "
                 "information refer to "
                 "https://lumicks-pylake.readthedocs.io/en/latest/tutorial/nbwidgets.html#migrating-old-track-files "
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
 
     version_header = f"Exported with pylake v{__version__} | track coordinates v4\n"
@@ -207,7 +208,7 @@ 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):
@@ -226,7 +227,8 @@ def create_track(time, coord, min_length=None):
                 "greater or equal to the minimum length used for the original tracking. For more "
                 "information refer to "
                 "https://lumicks-pylake.readthedocs.io/en/latest/tutorial/nbwidgets.html#migrating-old-track-files"
-            )
+            ),
+            stacklevel=find_stack_level(),
         )
         min_duration_field = "minimum_length (-)"
     else:
@@ -592,7 +594,7 @@ 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
@@ -905,7 +907,8 @@ 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
 
@@ -1634,7 +1637,8 @@ 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
 
@@ -1649,7 +1653,8 @@ 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
 
@@ -1678,7 +1683,7 @@ 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:
@@ -1861,10 +1866,11 @@ 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]
@@ -1925,6 +1931,7 @@ 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 4b21d6b24..d84441f57 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 find_kymograph_peaks, refine_peak_based_on_moment
 from .detail.gaussian_mle import gaussian_mle_1d, overlapping_pixels
 from .detail.trace_line_2d import detect_lines, points_to_line_segments
@@ -564,7 +565,8 @@ 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:
@@ -650,7 +652,10 @@ 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 46d49bfbf..fc4ee01c5 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,
@@ -52,7 +54,10 @@ 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 c5032c555..6d5567704 100644
--- a/lumicks/pylake/nb_widgets/kymotracker_widgets.py
+++ b/lumicks/pylake/nb_widgets/kymotracker_widgets.py
@@ -12,6 +12,8 @@
 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__(
@@ -343,7 +345,8 @@ 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 72e5758cd..3e20302db 100644
--- a/lumicks/pylake/piezo_tracking/piezo_tracking.py
+++ b/lumicks/pylake/piezo_tracking/piezo_tracking.py
@@ -4,6 +4,7 @@
 
 from ..channel import Slice
 from .baseline import ForceBaseLine
+from ..detail.utilities import find_stack_level
 
 __all__ = ["DistanceCalibration", "PiezoTrackingCalibration", "PiezoForceDistance"]
 
@@ -34,7 +35,8 @@ 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."
-                )
+                ),
+                stacklevel=find_stack_level(),
             )
 
         coeffs = np.polyfit(self.position, self.distance, degree)
diff --git a/lumicks/pylake/population/detail/hmm.py b/lumicks/pylake/population/detail/hmm.py
index 962413e0b..d534887c2 100644
--- a/lumicks/pylake/population/detail/hmm.py
+++ b/lumicks/pylake/population/detail/hmm.py
@@ -17,6 +17,7 @@
 from .fit_info import PopulationFitInfo
 from ...channel import Slice, Continuous
 from .validators import col, row
+from ...detail.utilities import find_stack_level
 
 
 def normalize_rows(matrix):
@@ -152,8 +153,11 @@ def baum_welch(data, model, tol, max_iter):
 
         if not converged:
             warnings.warn(
-                f"Model has not converged after {_itr} iterations. Last log likelihood step "
-                f"was {delta:0.4e}."
+                RuntimeWarning(
+                    f"Model has not converged after {_itr} iterations. Last log likelihood step "
+                    f"was {delta:0.4e}."
+                ),
+                stacklevel=find_stack_level(),
             )
 
     # free parameters; pi and each row of A constrained to sum to 1