First Tutorial¶

Converting all the images in a h5 file and saving them in a folder

#import package

from h5tiff.h5tiff import *
import flammkuchen as fl

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_1671/3490827386.py in <module>
      1 #import package
      2 
----> 3 from h5tiff.h5tiff import *
      4 import flammkuchen as fl

~/work/h5_tiff_converter/h5_tiff_converter/h5tiff/h5tiff.py in <module>
      4 import tifffile as tiff
      5 import numpy as np
----> 6 import tqdm
      7 from pathlib import Path
      8 

ModuleNotFoundError: No module named 'tqdm'

master_folder = r"/mnt/data/testing/2021_09_30_f0_line_52.h5"
save_name = "test"
mode = "LFM"
save_folder = "subfolder"   # or -> "Path("/my/path")"

file = H5File(master_folder,save_name,mode, save_folder)

print(  file.metadata.keys(), "\n",
        file.mode, "\n",
        file.path, "\n",
        file.save_name, "\n",
        file.save_folder)

dict_keys(['motorData', 'metadata', 'img_time']) 
 LFM 
 /mnt/data/testing/2021_09_30_f0_line_52.h5 
 test 
 subfolder

file.convert()

Saving: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 32/32 [00:18<00:00,  1.70it/s]

Conversion completed
Conversion completed

a = fl.load(master_folder)

a['metadata']

{'axis': ['x', 'y', 'z'],
 'ranges': [array([0.62, 0.68]),
  array([3.25, 3.35]),
  array([7.55      , 7.58285714, 7.61571429, 7.64857143, 7.68142857,
         7.71428571, 7.74714286, 7.78      ])],
 'start_pos': [0.62, 3.25, 7.55],
 'steps': [2, 2, 8],
 'fish_n': 0,
 'note': 'line 52',
 'start_time': 1633004492.3533864}

from tqdm import tqdm