feature: tem refactoring + tutorial notebook #87

jedyeo · 2022-03-10T10:07:55Z

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…actor

review-notebook-app · 2022-03-10T10:07:59Z

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geoffwoollard · 2022-03-10T22:34:13Z

This looks incomplete. I put some comments in https://app.reviewnb.com/compSPI/simSPI/pull/86/

geoffwoollard · 2022-03-23T20:47:01Z

notebooks/tem_tutorial.ipynb

@@ -0,0 +1,457 @@
+{


Ensure the outputs to the notebook are available/run in the committed version that is publicly available.

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geoffwoollard · 2022-03-23T20:47:01Z

notebooks/tem_tutorial.ipynb

@@ -0,0 +1,457 @@
+{


image not showing up

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…actor

…to address deepsource issue

ninamiolane

Thanks! LGTM, just one comment about why the descriptions of some parameters have been removed.

ninamiolane · 2022-03-24T23:05:31Z

tests/test_files/tem/sim_config.yaml

-    defocus_syst_error_um: 0.0       # [μm]
-    defocus_nonsyst_error_um: 0.0    # [μm]
-    optics_defocusout: None     # file to write defocus values
+    magnification: 81000             #


Why removing the descriptions of the parameters?

Thank you for catching this. These seem to have been accidentally removed during a merge conflict. The descriptions have been added back.

geoffwoollard · 2022-03-25T01:50:49Z

Hooray!!!

Look at that beautiful test coverage!

Look back and see how far you've come, enjoy, and imagine how this could come together in the time you have left.

Keep working hard!

---------- coverage: platform linux, python 3.9.12-final-0 -----------
Name                                          Stmts   Miss  Cover   Missing
---------------------------------------------------------------------------
simSPI/__init__.py                                1      0   100%
simSPI/crd.py                                    27      0   100%
simSPI/fov.py                                    76      0   100%
simSPI/linear_simulator/ctf.py                   37      0   100%
simSPI/linear_simulator/linear_simulator.py      33      0   100%
simSPI/linear_simulator/noise_utils.py            8      0   100%
simSPI/linear_simulator/params_utils.py          87      0   100%
simSPI/linear_simulator/projector.py             20      0   100%
simSPI/linear_simulator/shift_utils.py           22      0   100%
simSPI/linear_simulator/volume_utils.py           7      0   100%
simSPI/multislice.py                             31      0   100%
simSPI/tem.py                                   122      5    96%   192-193, 196, 242-246
simSPI/tem_distribution.py                       18      0   100%
simSPI/tem_inputs.py                            203      6    97%   354-355, 384-385, 504-505
simSPI/transfer.py                               52      3    94%   100, 107, [177](https://github.com/compSPI/simSPI/runs/5685549113?check_suite_focus=true#step:4:177)
---------------------------------------------------------------------------
TOTAL                                           744     14    98%
Coverage XML written to file coverage.xml

Required test coverage of 90.0% reached. Total coverage: 98.12%
================= 57 passed, 28 warnings in 637.83s (0:10:37) ==================

fredericpoitevin

Good work, guys!

fredericpoitevin · 2022-03-25T15:43:53Z

simSPI/tem_inputs.py

+    rotation_metadata : array-like, shape=[..., 3]
+        N x 3 matrix representing the rotation angles , phi, theta, psi, of
+        each particle in stack.


It would be useful to say which convention is used: XYX, ...?

fredericpoitevin · 2022-03-25T15:45:58Z

sim_config.yaml

@@ -7,6 +7,7 @@
    hole_diameter_nm: 1200         # [nm]
    hole_thickness_center_nm: 100  # [nm]
    hole_thickness_edge_nm: 100    # [nm]
+    particle_slice_pad: 5          #


# [pixel] ?

fredericpoitevin · 2022-03-25T15:46:15Z

sim_config.yaml

@@ -15,7 +16,7 @@
    electron_dose_std_e_per_nm2: 0   # standard deviation of dose per image

  optics_parameters:
-    magnification: 81000        #
+    magnification: 81000             #


review-notebook-app · 2022-03-25T16:47:14Z

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fredericpoitevin commented on 2022-03-25T16:47:14Z
----------------------------------------------------------------

Add link to reference paper: https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2011.03497.x

review-notebook-app · 2022-03-25T16:47:16Z

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fredericpoitevin commented on 2022-03-25T16:47:15Z
----------------------------------------------------------------

Some explanatory text would have been helpful.

arjunsingh3600 and others added 16 commits March 9, 2022 19:57

added todo in workflow

31e72eb

refactored get_image_data -> run

a7a4fc7

refactor

670e701

fixed docstring and tests

ab334c8

cleaned up docstrings and reviewed tests

0ea7c5e

Removed pad as parameter input, added to simulator config file.

28aaeaf

updated tem-input tests

659d3f6

Added pad to metadata file.

8b3576c

changed miscallenous -> noise_params

82a7586

merge

013b8b2

fixed typos

5897e9b

Updated test suite.

98c6682

Merge branch 'tem/refactor' of github.com:compSPI/simSPI into tem/ref…

91986f5

…actor

added demo notebook

e0947b1

gi

d999a50

notebook changes to reflect refactoring

1fcc8d4

arjunsingh3600 and others added 4 commits March 10, 2022 11:27

added todos

02dc81d

added upload

a178aaa

Added notebook descriptions for workflow.

2888c70

Notebook changes.

120a3fd

calhep added 8 commits March 14, 2022 15:24

Demonstration updates and refactor.

6d3010b

Moved static method to tem_inputs.

d5c154e

Added test suite for tem_tutorial notebook, more refactoring.

0194088

Updated notebook docstrings, dependencies.

c2cf4bc

Updated dependencies.

add6cad

Updated dependencies.

4ddb64e

Updated linting.

cef6fee

Updated formatting.

51171bc

geoffwoollard reviewed Mar 23, 2022

View reviewed changes

arjunsingh3600 added 14 commits March 23, 2022 20:44

updated test_tem_inputs path

d7aa793

Merge branch 'tem/refactor' of github.com:compSPI/simSPI into tem/ref…

f14310b

…actor

debugging statements

2931559

debuggin statements

07806a5

debugging

39981d5

run w/o cache

ecd9b3f

removed extra files

56df0dd

rerun w/o cache

ff10311

added input file check in tem_inputs

0028762

fixed extension in type check

3546f15

added file checks in tem_inputs

2b8184d

removed file check function and implemented code in relevant methods …

bfb4b88

…to address deepsource issue

Added file verification to tem.py

a2e31fe

Added some log statements. increased test coverage.

36e6792

jedyeo marked this pull request as ready for review March 24, 2022 23:03

ninamiolane approved these changes Mar 24, 2022

View reviewed changes

arjunsingh3600 and others added 4 commits March 24, 2022 16:14

addded sim_config descriptions back

7ff6578

added particle slice config

9a4d871

added missing parameters to sim_config

a977e94

Added notebook with images for user reference.

18b604c

geoffwoollard approved these changes Mar 25, 2022

View reviewed changes

jedyeo mentioned this pull request Mar 25, 2022

programmatic way to download datasets from OSF compSPI/ioSPI#48

Closed

Delete path_config-checkpoint.yaml

c8b861a

fredericpoitevin approved these changes Mar 25, 2022

View reviewed changes

fredericpoitevin merged commit b66f479 into master Mar 25, 2022

fredericpoitevin deleted the tem/refactor branch March 25, 2022 16:49

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feature: tem refactoring + tutorial notebook #87

feature: tem refactoring + tutorial notebook #87

jedyeo commented Mar 10, 2022

review-notebook-app bot commented Mar 10, 2022

geoffwoollard commented Mar 10, 2022

geoffwoollard Mar 23, 2022

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review-notebook-app bot commented Mar 25, 2022

review-notebook-app bot commented Mar 25, 2022 •

edited by fredericpoitevin

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feature: tem refactoring + tutorial notebook #87

feature: tem refactoring + tutorial notebook #87

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jedyeo commented Mar 10, 2022

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review-notebook-app bot commented Mar 25, 2022 • edited by fredericpoitevin Loading

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