examples/milopyp.md
... ...
@@ -0,0 +1,36 @@
1
+```
2
+#!/usr/bin/env bash
3
+
4
+## MiloPYP Quick tutorials
5
+## https://nextpyp.app/milopyp/quick_tutorial/
6
+##
7
+## Download tutorial data in cwd and run Cellular Content Exploration
8
+## Takes ~ 40 minutes on one NVIDIA GeForce GTX 1080 Ti
9
+##
10
+## James Vincent help@sbgrid.org
11
+## Nov 1, 2024
12
+
13
+export SBGRID_ALLOW=true # sbgrid internal only
14
+
15
+## Start SBGrid environment
16
+source /programs/sbgrid.shrc
17
+export MILOPYP_X=0.5.0
18
+
19
+## Set location of milopyp python scripts:
20
+milo_dir=/programs//x86_64-linux/milopyp/${MILOPYP_X}/cet_pick/cet_pick
21
+
22
+## Download globular tutorial data | Globular-shaped particles (EMPIAR-10304)
23
+wget https://nextpyp.app/files/data/milopyp_globular_tutorial.tbz
24
+tar xvfz milopyp_globular_tutorial.tbz
25
+mkdir data sample_data
26
+mv *.txt ./data
27
+mv *.rec *.ali *.tlt ./sample_data
28
+
29
+
30
+## -- Cellular content exploration module --
31
+
32
+## Training 2d3d
33
+python.milopyp ${milo_dir}/simsiam_main.py simsiam2d3d --num_epochs 20 --exp_id test_sample --bbox 36 --dataset simsiam2d3d --arch simsiam2d3d_18 --lr 1e-3 --train_img_txt sample_train_explore_img.txt --batch_size 256 --val_intervals 20 --save_all --gauss 0.8 --dog 3,5
34
+
35
+## Inference 2d3d
36
+python.milopyp ${milo_dir}/simsiam_test_hm_2d3d.py simsiam2d3d --exp_id test_sample --bbox 36 --dataset simsiam2d3d --arch simsiam2d3d_18 --test_img_txt sample_train_explore_img.txt --load_model exp/simsiam2d3d/test_sample/model_20.pth --gauss 0.8 --dog 3,5```