[Bug]: phantom traces

[LHolmes2]

Checklist

• [X] Re-run analysis with topostats process --core 1.
• [X] Describe the bug.
• [X] Include the configuration file.
• [X] Copy of the output.
• [X] The exact command that failed. This is what you typed at the command line, including any options.
• [X] TopoStats version, this is reported by topostats --version
• [X] Operating System and Python Version

Describe the bug

The traces appear in the wrong X,Y coordiantes.

Copy of the output

Include the configuration file

# Configuration from TopoStats run completed : 2024-02-05 12:10:34
# For more information on configuration and how to use it:
# https://afm-spm.github.io/TopoStats/main/configuration.html
base_dir: /Users/libbyholmes/Library/CloudStorage/[email protected]/Shared
  drives/Pyne Group/AFM_Data/Telomeres/20240201_pICOz_TEL12_shelterin
cores: 2
dnatracing: {min_skeleton_size: 10, pad_width: 1, run: true, skeletonisation_method: topostats,
  spline_circular_smoothing: 0.0, spline_linear_smoothing: 5.0, spline_step_size: 7e-09}
file_ext: .spm
filter:
  gaussian_mode: nearest
  gaussian_size: 0.0
  otsu_threshold_multiplier: 1.0
  remove_scars: {max_scar_width: 4, min_scar_length: 16, removal_iterations: 2, run: false,
    threshold_high: 0.666, threshold_low: 0.25}
  row_alignment_quantile: 0.5
  run: true
  threshold_absolute: {above: 1.0, below: -1.0}
  threshold_method: std_dev
  threshold_std_dev: {above: 1.0, below: 10.0}
grains:
  absolute_area_threshold:
    above: [300, 3000]
    below: [null, null]
  direction: above
  otsu_threshold_multiplier: 1.0
  remove_edge_intersecting_grains: true
  run: true
  smallest_grain_size_nm2: 50
  threshold_absolute: {above: 1.0, below: -1.0}
  threshold_method: std_dev
  threshold_std_dev: {above: 1.0, below: 10.0}
grainstats: {cropped_size: 40.0, edge_detection_method: binary_erosion, run: true}
loading: {channel: Height}
log_level: info
output_dir: /Users/libbyholmes/Library/CloudStorage/[email protected]/Shared
  drives/Pyne Group/AFM_Data/Telomeres/20240201_pICOz_TEL12_shelterin
plotting:
  axes: true
  colorbar: true
  histogram_log_axis: false
  image_set: core
  mask_cmap: blu
  num_ticks: [null, null]
  pixel_interpolation: null
  run: true
  save_format: png
  style: topostats.mplstyle
  zrange: [-2, 3]
summary_stats: {config: null, run: true}

To Reproduce

Run on main. File found in Shared drives/Pyne Group/Code/Topostats Error Files/Phantom traces/20240201_8ng_topo_picoz_tel12__KCLshelterinbuffer_mgni_eph.0_00018.spm

TopoStats Version

2.1.2

Python Version

3.11

Operating System

MacOS Intel (pre-2021)

Python Packages

asttokens==2.4.1
cheap-repr==0.5.1
contextlib2==21.6.0
contourpy==1.2.0
cycler==0.12.1
decorator==5.1.1
exceptiongroup==1.2.0
executing==2.0.1
fonttools==4.47.2
h5py==3.10.0
igor2==0.5.3
imageio==2.33.1
ipython==8.20.0
jedi==0.19.1
joblib==1.3.2
kiwisolver==1.4.5
lazy_loader==0.3
matplotlib==3.8.2
matplotlib-inline==0.1.6
networkx==3.2.1
numpy==1.26.3
packaging==23.2
pandas==2.2.0
parso==0.8.3
pexpect==4.9.0
pillow==10.2.0
prompt-toolkit==3.0.43
psutil==5.9.8
ptyprocess==0.7.0
pure-eval==0.2.2
pyfiglet==1.0.2
Pygments==2.17.2
pyparsing==3.1.1
pyspm==0.6.0
python-dateutil==2.8.2
pytz==2023.3.post1
PyYAML==6.0.1
ruamel.yaml==0.18.5
ruamel.yaml.clib==0.2.8
schema==0.7.5
scikit-image==0.22.0
scikit-learn==1.4.0
scipy==1.12.0
seaborn==0.13.1
six==1.16.0
snoop==0.4.3
stack-data==0.6.3
threadpoolctl==3.2.0
tifffile==2023.12.9
topofileformats==0.1.0
-e git+https://github.com/AFM-SPM/TopoStats.git@43410ab06bf366764271553a16f88d97f3c29999#egg=topostats
tqdm==4.66.1
traitlets==5.14.1
tzdata==2023.4
wcwidth==0.2.13

[ns-rse]

Thanks for the report @LHolmes2

You've indicated that you are using v2.1.2 of TopoStats but in the Python Packages list it suggests the version in the Conda environment was installed from Git on commit 43410ab06bf366764271553a16f88d97f3c29999 and the commit assoicated with v2.1.2 is 14cd56dd19eecc6af0ae105b076d51d3afe0bad3.

Would you be able to check that this still occurs with v2.2.post0 that was created last week please?

I'd recommend creating a new Conda environment for this. The following should work...

conda create -n topostats220
conda activate topostats220
pip install topostats       # This will install the latest version of TopoStats from PyPI

...and then re-run with your configuration file.

Ping on Slack if you have any problems with getting the Conda environment up and running.

[LHolmes2]

Hi @ns-rse , Thank you for the suggestion. I managed to do what you have suggested, however it doesn't seem to have fixed the issue. Still having strange traces, albeit different to the original traced file in this report.

[ns-rse]

Thanks for checking @LHolmes2

I'm struggling to map the masks to where they should be but have an idea that this may be caused with how these are aligned with the overall image.

Its on the ToDo list.

[Max-Gamill]

I also think this might cause the "failed to skeletonise error" and dnatracing stats for these molecules to not be captured:

[Max-Gamill]

going to assume this has been fixed internally due to lack of response :)