added fiber tracking and tested using Shooka Karimour's data

Readme.md

@@ -1,5 +1,5 @@
 December 25, 2022
-Version: 0.6.5
+Version: 0.7.0
 
 <img src="./user_manual/figs/logo.png" style="zoom:20%;" />
 
@@ -29,6 +29,7 @@ MyPTV is designed to be used by scientists and engineers who need to track the t
 6) Tracking particles in 2D
 7) Smoothing particle trajectories while calculating their velocities and accelerations
 8) Re-connecting broken trajectories
+9) Measuring the orientations of anisotropic particles in 3D (new from version 7.0.0 and on)
 
 ## How to install?
 

example/params_file.yml

@@ -10,6 +10,7 @@
     images_folder: Images_cam1
     single_image_name: cal2.tif
     image_extension: '.tif'
+    shape: particles
     mask: 1.0
     ROI: 227, 1050, 120, 920
     plot_result: True
@@ -24,7 +25,7 @@
     max_ysize: 15.0
     max_mass: None
     method: labeling
-    particle_size: 8
+    particle_size: 8  
     save_name: test
 
 - matching:
@@ -73,7 +74,6 @@
     max_distance: 0.4
     save_name: trajecotries_stitched
 
-
 - 2D_tracking:
     blob_file: blobs_cam1
     frame_start: 0
@@ -85,24 +85,20 @@
     dv_max: 1.0
     save_name: trajectories_2D
 
-
 - manual_matching_GUI:
     cameras: [cam1, cam2, cam3]
     images: [./Images_cam1/01.tif, ./Images_cam2/01.tif, ./Images_cam3/01.tif]
 
-
-# This is for fiber orientations, developed by Eric Aschari
-- orientations:
+- fiber_orientations:
     camera_names: cam1, cam2
     cam_resolution: 1248, 1248
     blob_files: blobs_cam1_direction, blobs_cam2_direction
     fibers_file: particles
     trajectory_file: trajectories
     save_name: fiber_orientations
 
-
-# Future preparation for adding external functionalities
 - run_extension:
     path_to_extention: the_absolute_path_to_the_script_containing_the_code 
     action_name: the_name_of_the_class_that_needs_to_run  
     extention_params_file: the_path_to_the_extentions_params_file
+

myptv/fibers/__init__.py

@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Sun March  20 2020
+
+@author: ron
+
+MyPTV init file
+"""
+
+
+
+

myptv/fiber_reconstruction/fiber_segmentation_mod.py → myptv/fibers/fiber_segmentation_mod.py

@@ -308,7 +308,7 @@ def get_blobs(self):
 
             stamp_y, stamp_x = meshgrid(range(self.im.shape[1]), 
                                         range(self.im.shape[0]))
-                        
+
             for blob in range(len(blob_pixels)):
 
                 index = np.argwhere(self.labeled == blob+1)/1.0
@@ -410,10 +410,11 @@ def apply_blobs_size_filter(self):
 
         if self.mass_limits[0] is not None:
             fltr = lambda b: b[2] > self.mass_limits[0]
+            self.blobs = list(filter(fltr, self.blobs))
 
         if self.mass_limits[1] is not None:
             fltr = lambda b: b[2] < self.mass_limits[1]
-
+            self.blobs = list(filter(fltr, self.blobs))
 
 
     def plot_blobs(self, vmin=None, vmax=None):

myptv/imaging_mod.py

@@ -43,7 +43,7 @@
 
 import os
 from math import sin, cos
-from numpy import zeros, array, dot
+from numpy import zeros, array, dot, transpose
 from numpy.linalg import inv
 from myptv.utils import line_dist, point_line_dist
 
@@ -229,6 +229,28 @@ def get_r(self, eta, zeta):
         return r
 
 
+    def get_r_ori(self, u): # from Eric
+        '''
+        A function used for the orientation of fibers, written 
+        by Eric Aschari.
+        
+        input - pixel coordinates (eta, zeta) seen by the camera
+        output - direction vector in real space
+        '''
+
+        eta = u[0,0]
+        zeta = u[1,0]
+
+        Z3 = [eta, zeta, eta**2, zeta**2, eta * zeta]
+
+        e = dot(self.E, Z3)
+
+        r = dot(array([-eta, -zeta, -self.f]) - e, self.R) # previously with - before eta_ and zeta_
+        r = r / (r[0]**2 + r[1]**2 + r[2]**2)**0.5
+
+        return transpose(array([self.O + r])) 
+
+
     def projection(self, x, correction=True):
         '''
         will return the image coordinate (eta, zeta) of a real point x.

setup.py

@@ -8,8 +8,8 @@
 
 setup(
     name='myptv',
-    packages=find_packages(include=['myptv']),
-    version='0.6.5',
+    packages=find_packages(include=['myptv', 'myptv.fibers']),
+    version='0.7.0',
     description='A 3D Particle Tracking Velocimetry library',
     install_requires=['numpy', 'scipy', 'scikit-image','pandas','matplotlib','pyyaml', 'tk', 'Pillow'],
     author='Ron Shnapp',