Added changes and files from lebpc34

Author: Stepp Willi Leopold

20201014_Mito2Drp1.ipynb

@@ -13,15 +13,11 @@
 from datetime import datetime
 
 
-
-
-
-
 if __name__ == "__main__":
     path = "//lebnas1.epfl.ch/microsc125/Watchdog/"
     filename = 'binary_output.dat'
     fullFileDir = path + filename
-    
+
     x = False
     x = bool(x)
     i = 0

binOutput.py

@@ -0,0 +1,32 @@
+%% Matlab script to try reading in a binary file that was output from the
+% python program that will be used to run the neural network
+function start_monitoring_NAS()
+%% Small GUI
+DlgH = figure('Position',[500 500 250 100],'Name','Matlab',...
+    'NumberTitle','off');
+H = uicontrol('Style', 'PushButton', 'String', 'Break',...
+    'Callback', 'delete(gcf)');
+Text = uicontrol('Style','text','Position',[100 0 200 100],...
+    'Background',[0.9 0.9 0.9],'FontSize',25);                
+ drawnow               
+
+%% While loop pulling the data from the network location
+x_old = 0;
+while (ishandle(H))
+    fileID = fopen('//lebnas1.epfl.ch/microsc125/Watchdog/binary_output.dat','r');
+    x = fread(fileID);
+    fclose(fileID);
+    x = size(x,1);
+    Text.String = num2str(x);
+    set(Text,'Background', [0.5 0.5 0.5] + (x/512));
+    if x ~= x_old
+        disp(x)
+        disp(datetime('now','TimeZone','local','Format','HH:mm:ss.SSS'))
+    end
+    x_old = x;
+    pause(0.01)
+end
+
+end
+
+

readBinNetwork.m

@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+"""
+Created on 201102
+
+@author: stepp
+
+Application to read a h5 file and save a tif from it at 2Hz to test the
+watchdog on lebpc20
+"""
+
+import time
+import numpy as np
+import matplotlib.pyplot as plt
+import h5py
+from skimage import io
+import os
+
+data_path = 'C:/Users/stepp/Documents/data_raw/SmartMito/'  # nb: begin with /
+print('data_path : ', data_path)
+print()
+input_data_filename1 = data_path + 'Mito.h5'  # Mito
+input_data_filename2 = data_path + 'Drp1.h5'  # Drp1
+
+input_data_filename1 = data_path + 'cell_8_Pos1_mito_741.tif'  # Mito
+input_data_filename2 = data_path + 'cell_8_Pos1_drp1_741.tif'  # Drp1
+
+# input_data_filename1 = data_path + 'cell_8_mito_1024.tif'  # Mito
+# input_data_filename2 = data_path + 'cell_8_drp1_1024.tif'  # Drp1
+
+# input_data_filename1 = data_path + 'cell_8_mito.tif'  # Mito
+# input_data_filename2 = data_path + 'cell_8_drp1.tif'  # Drp1
+
+# input_data_filename1 = data_path + 's3_c6_mito.tif'  # Mito
+# input_data_filename2 = data_path + 's3_c6_drp1.tif'  # Drp1
+
+mito = []
+drp = []
+
+if input_data_filename1[-3:] == '.h5':
+    hf = h5py.File(input_data_filename1, 'r')
+    mito = hf.get('Mito')  # Mito
+else:
+    mito = io.imread(input_data_filename1)
+
+print(mito.dtype)
+print('Input : ', mito.shape)
+print('Input : ', np.shape(mito)[0])
+
+if input_data_filename2[-3:] == '.h5':
+    hf = h5py.File(input_data_filename2, 'r')
+    drp = hf.get('Drp1')
+else:
+    drp = io.imread(input_data_filename2)
+
+print(drp.dtype)
+print('Input : ', drp.shape)
+print('Input : ', np.shape(drp)[0])
+
+nas_path = '//lebnas1.epfl.ch/microsc125/Watchdog/python_saver/'
+
+i = 0
+for item in range(200, 213):
+    # for item in range(1, 2002, 1000):  # [1, 208]:  # range(150, 210):
+    t1 = time.perf_counter()
+    print(item)
+    mito_path = nas_path + 'img_channel000_position000_time' + \
+        str((i*2)).zfill(9) + '_z000.tiff'
+    drp_path = nas_path + 'img_channel000_position000_time' + \
+        str((i*2 + 1)).zfill(9) + '_z000.tiff'
+
+    # First write mito then drp as watchdog waits for drp image
+    io.imsave(mito_path, mito[item, :, :].astype(np.uint16),
+              check_contrast=False)
+    time.sleep(0.05)
+    io.imsave(drp_path, drp[item, :, :].astype(np.uint16),
+              check_contrast=False)
+    t2 = time.perf_counter()
+    time.sleep(np.max([0, .45 - (t2 - t1)]))
+    i = i + 1
+
+time.sleep(3)
+
+# Clear the folder completely to have the same situation always
+for f in os.listdir(nas_path):
+    if not f.endswith(".tiff"):
+        continue
+    os.remove(os.path.join(nas_path, f))