spacr 0.3.2__py3-none-any.whl → 0.3.3__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (19) hide show
  1. spacr/core.py +105 -1
  2. spacr/deep_spacr.py +191 -141
  3. spacr/gui.py +1 -0
  4. spacr/gui_core.py +13 -4
  5. spacr/gui_utils.py +29 -1
  6. spacr/io.py +84 -125
  7. spacr/measure.py +1 -38
  8. spacr/ml.py +153 -66
  9. spacr/plot.py +429 -7
  10. spacr/settings.py +55 -10
  11. spacr/submodules.py +7 -6
  12. spacr/toxo.py +9 -4
  13. spacr/utils.py +510 -16
  14. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/METADATA +28 -25
  15. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/RECORD +19 -19
  16. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/LICENSE +0 -0
  17. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/WHEEL +0 -0
  18. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/entry_points.txt +0 -0
  19. {spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/top_level.txt +0 -0
{spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: spacr
3
- Version: 0.3.2
3
+ Version: 0.3.3
4
4
  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
5
5
  Home-page: https://github.com/EinarOlafsson/spacr
6
6
  Author: Einar Birnir Olafsson
@@ -10,34 +10,41 @@ Classifier: License :: OSI Approved :: MIT License
10
10
  Classifier: Operating System :: OS Independent
11
11
  Description-Content-Type: text/x-rst
12
12
  License-File: LICENSE
13
- Requires-Dist: torch<3.0,>=2.0
14
- Requires-Dist: torchvision<1.0,>=0.1
15
- Requires-Dist: torch-geometric<3.0,>=2.5
16
13
  Requires-Dist: numpy<2.0,>=1.26.4
17
- Requires-Dist: bottleneck<2.0,>=1.3.6
18
- Requires-Dist: numexpr<3.0,>=2.8.4
19
14
  Requires-Dist: pandas<3.0,>=2.2.1
20
- Requires-Dist: statsmodels<1.0,>=0.14.1
15
+ Requires-Dist: scipy<2.0,>=1.12.0
16
+ Requires-Dist: cellpose<4.0,>=3.0.6
21
17
  Requires-Dist: scikit-image<1.0,>=0.22.0
22
18
  Requires-Dist: scikit-learn<2.0,>=1.4.1
23
- Requires-Dist: seaborn<1.0,>=0.13.2
24
- Requires-Dist: matplotlib<4.0,>=3.8.3
25
- Requires-Dist: shap<1.0,>=0.45.0
26
- Requires-Dist: pillow<11.0,>=10.2.0
27
- Requires-Dist: imageio<3.0,>=2.34.0
28
- Requires-Dist: scipy<2.0,>=1.12.0
29
- Requires-Dist: ipywidgets<9.0,>=8.1.2
30
19
  Requires-Dist: mahotas<2.0,>=1.4.13
31
20
  Requires-Dist: btrack<1.0,>=0.6.5
32
21
  Requires-Dist: trackpy<1.0,>=0.6.2
33
- Requires-Dist: cellpose<4.0,>=3.0.6
34
- Requires-Dist: IPython<9.0,>=8.18.1
22
+ Requires-Dist: statsmodels<1.0,>=0.14.1
23
+ Requires-Dist: shap<1.0,>=0.45.0
24
+ Requires-Dist: torch<3.0,>=2.0
25
+ Requires-Dist: torchvision<1.0,>=0.1
26
+ Requires-Dist: torch-geometric<3.0,>=2.5
27
+ Requires-Dist: torchcam<1.0,>=0.4.0
28
+ Requires-Dist: transformers<5.0,>=4.45.2
29
+ Requires-Dist: segmentation-models-pytorch>=0.3.3
30
+ Requires-Dist: monai>=1.3.0
31
+ Requires-Dist: captum<1.0,>=0.7.0
32
+ Requires-Dist: seaborn<1.0,>=0.13.2
33
+ Requires-Dist: matplotlib<4.0,>=3.8.3
34
+ Requires-Dist: adjustText<2.0,>=1.2.0
35
+ Requires-Dist: bottleneck<2.0,>=1.3.6
36
+ Requires-Dist: numexpr<3.0,>=2.8.4
35
37
  Requires-Dist: opencv-python-headless<5.0,>=4.9.0.80
38
+ Requires-Dist: pillow<11.0,>=10.2.0
39
+ Requires-Dist: tifffile>=2023.4.12
40
+ Requires-Dist: nd2reader<4.0,>=3.3.0
41
+ Requires-Dist: czifile
42
+ Requires-Dist: imageio<3.0,>=2.34.0
43
+ Requires-Dist: pingouin<1.0,>=0.5.5
36
44
  Requires-Dist: umap-learn<1.0,>=0.5.6
37
45
  Requires-Dist: ttkthemes<4.0,>=3.2.2
38
46
  Requires-Dist: xgboost<3.0,>=2.0.3
39
47
  Requires-Dist: PyWavelets<2.0,>=1.6.0
40
- Requires-Dist: torchcam<1.0,>=0.4.0
41
48
  Requires-Dist: ttf-opensans>=2020.10.30
42
49
  Requires-Dist: customtkinter<6.0,>=5.2.2
43
50
  Requires-Dist: biopython<2.0,>=1.80
@@ -50,19 +57,15 @@ Requires-Dist: tables<4.0,>=3.8.0
50
57
  Requires-Dist: rapidfuzz<4.0,>=3.9
51
58
  Requires-Dist: keyring<16.0,>=15.1
52
59
  Requires-Dist: screeninfo<1.0,>=0.8.1
53
- Requires-Dist: ipykernel
54
- Requires-Dist: gdown
55
60
  Requires-Dist: fastremap>=1.14.1
56
- Requires-Dist: monai>=1.3.0
57
61
  Requires-Dist: pytz>=2023.3.post1
58
- Requires-Dist: segmentation-models-pytorch>=0.3.3
59
- Requires-Dist: tifffile>=2023.4.12
60
62
  Requires-Dist: tqdm>=4.65.0
61
63
  Requires-Dist: wandb>=0.16.2
62
64
  Requires-Dist: openai<2.0,>=1.50.2
63
- Requires-Dist: nd2reader<4.0,>=3.3.0
64
- Requires-Dist: czifile
65
- Requires-Dist: adjustText<2.0,>=1.2.0
65
+ Requires-Dist: gdown
66
+ Requires-Dist: IPython<9.0,>=8.18.1
67
+ Requires-Dist: ipykernel
68
+ Requires-Dist: ipywidgets<9.0,>=8.1.2
66
69
  Requires-Dist: huggingface-hub<0.25,>=0.24.0
67
70
  Provides-Extra: dev
68
71
  Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
{spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/RECORD RENAMED
@@ -8,26 +8,26 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
8
8
  spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
9
9
  spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
10
10
  spacr/cellpose.py,sha256=zv4BzhaP2O-mtQ-pUfYvpOyxgn1ke_bDWgdHD5UWm9I,13942
11
- spacr/core.py,sha256=KNsjpQR_L5mAABrJ4U_JMNsUMav81ILvnjL0Jf2ohU8,43858
12
- spacr/deep_spacr.py,sha256=HT7x_xHoM8s-AX6aSEHv4mf4wMld9PNDTgzsX-0FqO4,39416
13
- spacr/gui.py,sha256=ndmWP4F0QO5j6DM6MNzoGtzv_7Yj4LTW2SLi9URBZIQ,8055
14
- spacr/gui_core.py,sha256=OJQxzpehIyDzjSjIsvxSHat4NIjkqjX0VZAUQTnzEzg,40921
11
+ spacr/core.py,sha256=G_x-w7FRIHNfSOoPaIZPSf_A7mVj7PA7o9HQZ4nIu5o,48231
12
+ spacr/deep_spacr.py,sha256=HdOcNU8cHcE_19nP7_5uTz-ih3E169ffr2Hm--NvMvA,43255
13
+ spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
14
+ spacr/gui_core.py,sha256=LV_HX5zreu3Bye6sQFDbOuk8Dfj4StMoohy6hsrDEXA,41363
15
15
  spacr/gui_elements.py,sha256=3ru8FPZtXCZSj7167GJj18-Zo6TVebhAzkit-mmqmTI,135342
16
- spacr/gui_utils.py,sha256=76utRICvY0k_6X8CA1P_TmYBJARp4b87OkI9t39tldA,45822
17
- spacr/io.py,sha256=_P0Rb1ftBlheb9Yd0Bm8py_MeV2bh0ZxDlVRYOZAfBY,144579
16
+ spacr/gui_utils.py,sha256=hY7JC8HMlyKa9d7tDjkgXgRILgBYTw85jAkRsexO0P0,46960
17
+ spacr/io.py,sha256=AARmqn1fMmTgVDwWy8bEYK6SjH-6DZIulgCSPdBTyf0,143370
18
18
  spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
19
- spacr/measure.py,sha256=8MRjQdB-2n8JVLjEpF3cxvfT-Udug27uJ2ErJJ5t1ic,56000
19
+ spacr/measure.py,sha256=BThn_sALgKrwGKnLOGpT4FyoJeRVoTZoP9SXbCtCMRw,54857
20
20
  spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
21
- spacr/ml.py,sha256=uf43GIxxgSasq9OiWQYnQO0fV3d5yTPEHkV78jHb-i4,42540
21
+ spacr/ml.py,sha256=3XiQUfhhseCz9cZXhaVkCCv_qfqoZCdXGnO_p3ulwo4,47131
22
22
  spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
23
- spacr/plot.py,sha256=kPVUlMaRSH2zZIm64o8FmhHILMCRRmzs-uFVPQEIupw,85281
23
+ spacr/plot.py,sha256=eZcs-CQrDTENXVeMY8y8N8VZnmPePO-kAWdoaweFmW8,105540
24
24
  spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
25
- spacr/settings.py,sha256=IaRnHXRVrkOOfA0ymavXOJTjPE56_BdOPrbEHq7oONQ,73508
25
+ spacr/settings.py,sha256=BUQv8mSQLaw3yT08cKB0x5Y5gl0-S7AxmV6TABoPQlk,75773
26
26
  spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
27
- spacr/submodules.py,sha256=ojBFEnOZ_YTGcOvSFEAPP6J7-w08QIAFJLEPYjUCkMM,18337
27
+ spacr/submodules.py,sha256=AB7s6-cULsaqz-haAaCtXfGEIi8uPZGT4xoCslUJC3Y,18391
28
28
  spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
29
- spacr/toxo.py,sha256=nkV8w1wvaEsDFoSIOVvU5UcIIaTngHfgKNhhZYzBDyY,9893
30
- spacr/utils.py,sha256=nW4s7wy4spk3T3yYTQGLvonDz5KX6t_d0NKiHcqMPN0,193044
29
+ spacr/toxo.py,sha256=us3pQyULtMTyfTq0MWPn4QJTTmQ6BwAJKChNf75jo3I,10082
30
+ spacr/utils.py,sha256=w4Cht32Mhep7jfXKm5CSpyFLB3lOxiBCQI6PnaYcI3Q,213360
31
31
  spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
32
32
  spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
33
33
  spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -150,9 +150,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
150
150
  spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
151
151
  spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
152
152
  spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
153
- spacr-0.3.2.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
154
- spacr-0.3.2.dist-info/METADATA,sha256=T4leZtOLZyUy19ueD2g_TmAQdTRCbkS29QJXcVf6ciw,5837
155
- spacr-0.3.2.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
156
- spacr-0.3.2.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
157
- spacr-0.3.2.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
158
- spacr-0.3.2.dist-info/RECORD,,
153
+ spacr-0.3.3.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
154
+ spacr-0.3.3.dist-info/METADATA,sha256=GM--JU9SkgF8zTlY57176FMUgf_SdLe8Uy0YMb9-p4o,5948
155
+ spacr-0.3.3.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
156
+ spacr-0.3.3.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
157
+ spacr-0.3.3.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
158
+ spacr-0.3.3.dist-info/RECORD,,
{spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/LICENSE RENAMED
File without changes
{spacr-0.3.2.dist-info → spacr-0.3.3.dist-info}/WHEEL RENAMED
File without changes