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Fix_function_category#155

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pr4deepr wants to merge 122 commits intohaesleinhuepf:mainhaesleinhuepf/human-eval-bia:mainfrom pr4deepr:fix_function_categorypr4deepr/human-eval-bia:fix_function_categoryCopy head branch name to clipboard

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Commits

Commits on Jul 8, 2024

• create linear_intensity_profile.ipynb haesleinhuepf#36

  marabuuu

  committed
  b716e1e

Commits on Jul 17, 2024

• update linear_intensity_profile haesleinhuepf#36

  marabuuu

  committed
  392ced5

• add docstring haesleinhuepf#36

  marabuuu

  committed
  dd15f53

Commits on Jul 31, 2024

• Added identify_centroids evaluation task

  shinzlet

  committed
  b5ac5ff

• Add find_closest_neighbors test

  shinzlet

  committed
  a15bc40

Commits on Aug 1, 2024

• Added load_bgr_tif_and_output_rgb test case

  shinzlet

  committed
  9de0ca0

Commits on Aug 2, 2024

• Merge pull request haesleinhuepf#82 from marabuuu/linear-intensity-profile

  Show description for 2228801
  haesleinhuepf

  authored
  2228801

• Adjusted floating point comparison to account for error, made dtype explicit on image data

  shinzlet

  committed
  e4e43ac

Commits on Aug 4, 2024

• Add local_maxima_from_distance_transform test case

  ilan-theodoro

  committed
  5c236be

Commits on Aug 5, 2024

• Add flow_field_deformation test case

  ilan-theodoro

  committed
  f2114b2

• Add detect_ellipse test case

  ilan-theodoro

  committed
  2b1e508

Commits on Aug 7, 2024

• Fix typo

  JoOkuma

  committed
  9db4767

• readme typo

  JoOkuma

  committed
  ed76d68

• Adding test case for selecting cells that co-express some gene (intensity)

  JoOkuma

  committed
  18bfa09

• clean up jupyter outputs

  JoOkuma

  committed
  161cc05

• Add new test to register 3D timelapses

  JoOkuma

  committed
  7843c13

Commits on Aug 10, 2024

• added two test cases: gaussian fit to spot, and distance between two image maxima

  

  Teun Huijben

  authored and

  Teun Huijben

  committed
  68ce25e

Commits on Aug 12, 2024

• Merge pull request haesleinhuepf#87 from JoOkuma/fix-positive-typo

  Show description for aef5fc4
  haesleinhuepf

  authored
  aef5fc4

• more detailed prompt, more asserts

  haesleinhuepf

  committed
  e3ded1c

• Merge branch 'main' of https://github.com/shinzlet/human-eval-bia into pr/85

  haesleinhuepf

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  0c9e9aa

• rerun notebook

  haesleinhuepf

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  5463133

• renamed and rerun notebook

  haesleinhuepf

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  5c2aa76

• Merge pull request haesleinhuepf#85 from shinzlet/main

  Show description for f41b084
  haesleinhuepf

  authored
  f41b084

• made test more flexible, added test-cases

  haesleinhuepf

  committed
  2f889ce

• tiny documentation update

  haesleinhuepf

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  1ea7faa

• test ignoring order of points, return points as list of coordinates

  haesleinhuepf

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  9e35fda

• Merge pull request haesleinhuepf#86 from ilan-theodoro/main

  Show description for f30008c
  haesleinhuepf

  authored
  f30008c

• add another example assert, rerun notebook

  haesleinhuepf

  committed
  90e2d67

• Merge pull request haesleinhuepf#91 from TeunHuijben/two-test-cases

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  haesleinhuepf

  authored
  79fb8cc

• reran notebook

  haesleinhuepf

  committed
  fc5caf4

• be more precise in the docstring

  haesleinhuepf

  committed
  747b08b

• Merge pull request haesleinhuepf#90 from JoOkuma/registration

  Show description for 0bc2d53
  haesleinhuepf

  authored
  0bc2d53

• more precise docstring

  haesleinhuepf

  committed
  84fb711

• Merge pull request haesleinhuepf#88 from JoOkuma/cell-coexp

  Show description for 25f3947
  haesleinhuepf

  authored
  25f3947

Commits on Aug 13, 2024

• Added FFT spectrum testcase. It is a hard one :-)

  royerloic

  committed
  3e39781

• Addressed feedback from Robert.

  royerloic

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  4e0da0c

• Addressed feedback from Robert and fixed typos

  royerloic

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  812cca7

Commits on Aug 27, 2024

• add test case translate 3d image haesleinhuepf#7

  marabuuu

  committed
  269abcb

Commits on Aug 29, 2024

• update function name in check function haesleinhuepf#7

  marabuuu

  committed
  d574186

Commits on Sep 3, 2024

• test case for image histogram

  pr4deepr

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  8fb18cf

• updated to include num_bins as argument

  pr4deepr

  committed
  4d65794

• Merge pull request haesleinhuepf#105 from pr4deepr/main

  Show description for a5c5af9
  haesleinhuepf

  authored
  a5c5af9

• Update open_image_return_dimensions.ipynb

  Show description for bbab4a5
  tischi

  authored
  bbab4a5

• Merge pull request haesleinhuepf#106 from haesleinhuepf/tischi-patch-1

  Show description for fa5b2bf
  haesleinhuepf

  authored
  fa5b2bf

• reran the notebook

  haesleinhuepf

  committed
  78ffd66

• Merge pull request haesleinhuepf#94 from royerloic/main

  Show description for bdce242
  haesleinhuepf

  authored
  bdce242

• renamed notebook, simplified docstring

  haesleinhuepf

  committed
  2f3f096

• Merge pull request haesleinhuepf#101 from marabuuu/translate-image

  Show description for 56c749d
  haesleinhuepf

  authored
  56c749d

• save_image_voxel_size notebook

  pr4deepr

  committed
  d4e38f8

Commits on Sep 4, 2024

• modified function to save the image and return save path

  pr4deepr

  committed
  346a023

Commits on Sep 5, 2024

• creating new categories

  pr4deepr

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  cc70493

Commits on Sep 6, 2024

• ensured all tasks are in categories. Plot results

  pr4deepr

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  ae8e242

• remove all samples and result data except gpt-4o-2024-05-13, deepseek-coder-v2 and reference

  haesleinhuepf

  committed
  9c6cd9d

• rephrased almost all prompts, to have more precise type hints

  Show description for bd5d6c6
  haesleinhuepf

  committed
  bd5d6c6

• renamed old result files file to have "_old_prompt" in their model name

  haesleinhuepf

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  798e99a

• regenerated prompt list and problem file with new prompts

  haesleinhuepf

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  2df0b84

• recreated samples for gpt-4o2024-05-13 and reference

  haesleinhuepf

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  535d60b

• sampled deepseek-coder-v2 with new prompts

  haesleinhuepf

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  462d6c9

• evaluated samples

  haesleinhuepf

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  3a09c4f

• redraw all figures with old and new prompts comparison

  haesleinhuepf

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  997c218

Commits on Sep 7, 2024

• Fixed sum_intensity_projection docstring

  ian-coccimiglio

  committed
  ce54212

• Merge pull request haesleinhuepf#117 from ian-coccimiglio/fix_docstring

  Show description for cf639aa
  haesleinhuepf

  authored
  cf639aa

• fix sum images notebook to add two images rather than lists

  ian-coccimiglio

  committed
  5208a15

Commits on Sep 8, 2024

• add interpolate_stack.ipynb haesleinhuepf#6

  marabuuu

  committed
  1106276

Commits on Sep 9, 2024

• Fixed functions requesting images providing lists

  ian-coccimiglio

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  8b81759

• More flexible standard deviation acceptance

  ian-coccimiglio

  committed
  c2dac0a

• Allowed flexible interpretation of image dimensions based on PIL or Numpy

  ian-coccimiglio

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  f3fd45d

• Removed extra blocks

  ian-coccimiglio

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  4173d72

• replace function with np.linspace to allow more intermediate slices haesleinhuepf#6

  marabuuu

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  380fecc

• add categorise_functions yaml

  pr4deepr

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  d91385f

• Code to check if all test cases in yaml file

  pr4deepr

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  8a6b51b

• removed old files

  pr4deepr

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  48b164f

• read new yaml file and plot model performance by category

  pr4deepr

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  de3de62

• updated pull request template

  pr4deepr

  committed
  c2bf2ae

Commits on Sep 10, 2024

• update dock string haesleinhuepf#6

  Show description for e2ba3f6
  

  marabuuu

  and

  haesleinhuepf

  authored
  e2ba3f6

• test case for scaling and affine transform

  pr4deepr

  committed
  6ae01fa

• Merge branch 'haesleinhuepf:development-collecting-new-test-cases' into development-collecting-new-test-cases

  pr4deepr

  authored
  ccc37b1

• scale image affine transform test case

  pr4deepr

  committed
  77bcb51

Commits on Sep 11, 2024

• remove print statement and added clarity for return values

  pr4deepr

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  d5bda33

• cleared outputs

  pr4deepr

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  84a923c

• polygon and multipolygon test cases shapely

  pr4deepr

  committed
  f6646dc

• Revert "scale image affine transform test case"

  Show description for e255420
  pr4deepr

  committed
  e255420

• Merge pull request haesleinhuepf#132 from pr4deepr/shapely

  Show description for fb12e77
  haesleinhuepf

  authored
  fb12e77

• remove comment, too obvious

  haesleinhuepf

  authored
  07dbe46

• remove comment

  haesleinhuepf

  authored
  d0639d7

• just added another simple assert

  haesleinhuepf

  committed
  67608cf

• Merge pull request haesleinhuepf#125 from marabuuu/interpolate-stack

  Show description for 2e89826
  haesleinhuepf

  authored
  2e89826

• rename notebook, format prompt

  haesleinhuepf

  committed
  603fdc0

• Merge pull request haesleinhuepf#110 from pr4deepr/development-collecting-new-test-cases

  Show description for 3adede0
  haesleinhuepf

  authored
  3adede0

Commits on Sep 12, 2024

• Updated label images for more flexible inputs

  ian-coccimiglio

  committed
  3d7003f

Commits on Sep 13, 2024

• clean rerun notebook

  haesleinhuepf

  committed
  128fe25

• Merge pull request haesleinhuepf#126 from ian-coccimiglio/fix_stdev

  Show description for 4b1cc18
  haesleinhuepf

  authored
  4b1cc18

• Reverted change to workflow_batch_process_folder_count_labels

  ian-coccimiglio

  committed
  b0b37fb

Commits on Oct 14, 2024

• updated test cases jsonl + readme

  haesleinhuepf

  committed
  54dafef

Commits on Oct 17, 2024

• Added new cases studies for metadata reading plus some image analysis snippets

  rmassei

  committed
  d6416b4

Commits on Oct 18, 2024

• Correct the prompting of the new test cases

  rmassei

  committed
  115d08a

Commits on Nov 21, 2024

• Remove test-case which didnt pass

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  haesleinhuepf

  committed
  0a062eb

• Remove test which seems impossible to pass

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  haesleinhuepf

  committed
  8594164

• remove dyfunctional test-case

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  haesleinhuepf

  committed
  988338d

• remove test with to simple assert statements

  Show description for 384a9c3
  haesleinhuepf

  committed
  384a9c3

• renamed notebooks and functions, executed notebooks, refined docstrings

  haesleinhuepf

  committed
  39915c0

• Merge pull request haesleinhuepf#142 from rmassei/main

  Show description for e0c2df7
  haesleinhuepf

  authored
  e0c2df7

• Merge branch 'main' into pr/129

  haesleinhuepf

  committed
  9bee740

• reran notebook

  haesleinhuepf

  committed
  db2e3fd

• Merge pull request haesleinhuepf#129 from pr4deepr/function_categorize

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  haesleinhuepf

  authored
  d4ab9f8

• Merge pull request haesleinhuepf#134 from ian-coccimiglio/bfix_label

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  haesleinhuepf

  authored
  fa65fe7

• Merge pull request haesleinhuepf#127 from ian-coccimiglio/bfix_imdim

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  haesleinhuepf

  authored
  1117b11

• Merge branch 'main' into prompt-refinement

  haesleinhuepf

  committed
  8f3e180

• sync with dev branch

  haesleinhuepf

  committed
  ca19c87

• sync with dev branch

  haesleinhuepf

  committed
  683ad2e

• Merge branch 'development-collecting-new-test-cases' into prompt-refinement

  haesleinhuepf

  authored
  f33b93a

• Merge pull request haesleinhuepf#118 from haesleinhuepf/prompt-refinement

  Show description for 861114b
  haesleinhuepf

  authored
  861114b

• Merge pull request haesleinhuepf#121 from ian-coccimiglio/fix_sum_images

  Show description for 875a81d
  haesleinhuepf

  authored
  875a81d

• deleted all sample files

  haesleinhuepf

  committed
  4cc51e9

• Merge branch 'development-collecting-new-test-cases' of https://github.com/haesleinhuepf/human-eval-bia into development-collecting-new-test-cases

  haesleinhuepf

  committed
  d12113b

• deleted all sample files

  haesleinhuepf

  committed
  17130bb

• remove test case which didn't pass

  Show description for 87913fd
  haesleinhuepf

  committed
  87913fd

• test-case formatting

  haesleinhuepf

  committed
  d2a5fb0

• categorised new test-cases, re-generated jsonl file + readme

  haesleinhuepf

  committed
  7bc4208

• sampled reference, redraw plots

  haesleinhuepf

  committed
  c040396

• update documentation

  haesleinhuepf

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  2117f80

Commits on Nov 27, 2024

• fixed summarize by case notebook for reference

  pr4deepr

  committed
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