derollins
commented
1 year ago Update:
When run on nanocharacterisation lab analysis PC (PC that isn't my laptop above) on 3 cores with image set: all, 50 images out of 69 successfully processed.
Config file:
# Sample configuration file auto-generated : 2023-05-26 09:29:17
# For more information on configuration : https://afm-spm.github.io/TopoStats/main/configuration.html
base_dir: C:\Users\NanoLab\Desktop\TopoStats-User-Data\Eddie\DNA_Cas9
output_dir: C:\Users\NanoLab\Desktop\TopoStats-User-Data\Eddie\DNA_Cas9\outputabs1_65_3cores
log_level: info
cores: 3
file_ext: .spm
loading:
channel: Height
filter:
run: true
row_alignment_quantile: 0.5
threshold_method: std_dev
otsu_threshold_multiplier: 1.0
threshold_std_dev:
below: 10.0
above: 1.0
threshold_absolute:
below: -1.0
above: 1.0
gaussian_size: 1.0121397464510862
gaussian_mode: nearest
remove_scars:
run: true
removal_iterations: 2
threshold_low: 0.25
threshold_high: 0.666
max_scar_width: 4
min_scar_length: 16
grains:
run: true
threshold_method: absolute
otsu_threshold_multiplier: 1.0
threshold_std_dev:
below: 10.0
above: 1.0
threshold_absolute:
below: -1.0
above: 1.65
direction: above
smallest_grain_size_nm2: 50
absolute_area_threshold:
above:
- 100
- 500
below:
-
-
grainstats:
run: true
edge_detection_method: binary_erosion
cropped_size: 40.0
dnatracing:
run: true
min_skeleton_size: 10
plotting:
run: true
save_format: png
pixel_interpolation:
image_set: all
zrange:
- -4
- 4
colorbar: true
axes: true
cmap: nanoscope
mask_cmap: blu
histogram_log_axis: false
histogram_bins: 200
dpi: 1000
summary_stats:
run: true
config:
Log files: DNA_Cas9-2023-06-01-14-49-39.log DNA_Cas9-2023-06-01-14-49-44.log
Everything else the same.
Checklist
Please try and tick off each of these items when filing the bug report. There are further instructions on each below.
run_topostats --core 1.run_topostats --versionDescribe the bug
When run on 6 cores 50 out of 69 files from a particular dataset are processed successfully however when run on 3 cores 67 images are successfully processed with the other config parameters remaining unchanged. I also ran the same dataset and config with 3 cores on a different PC and got 67/69 successes on that.
Copy of the output
6 cores:
3 cores:
My laptop 3 cores:
Include the configuration file
If no configuration file was specified with the
-c/--config-fileoption the defaults were used, please use therun_topostats --create-config-file crash.yamlto save these to thecrash.yamlfile and copy the contents below.6 cores
3 cores:
My laptop 3 cores:
To Reproduce
If it is possible to share the file (e.g. via cloud services) that caused the error that would greatly assist in reproducing and investigating the problem. In addition the exact command used that failed should be pasted below.
Data is unpublished- contact me if required.
Output
Any output files that have been produced can be attached to this bug report (by default they will be under the
outputdirectory unless you have customised the configuration). 6cores: DNA_Cas9-2023-06-01-12-07-48.log DNA_Cas9-2023-06-01-12-07-55.log3cores:
DNA_Cas9-2023-06-01-14-20-23.log DNA_Cas9-2023-06-01-14-20-30.log
My laptop 3 cores: DNA_Cas9-2023-06-01-01-09-04.log DNA_Cas9-2023-06-01-01-09-15.log
TopoStats version
Please report the version of TopoStats you are using. There are several ways of doing this, either with
piporrun_topostats. Please copy and paste all output from either of the following commands.pip show topostatsrun_topostats --versionOperating System and Python Version
Operating System
Please let us know what operating system you are using, if you have used more than one then tick all boxes.
Python Version
Please let us know the version of Python you are using, paste the results of
python --versionOptional : Python Packages
If you are able to provide a list of your installed packages that may be useful. The best way to get this is to copy and paste the results of typing
pip freeze.Additional context
Add any other context about the problem here.