Merge pull request #31 from alexlib/pyptv3

First Python 3 compatible version

.travis.yml

@@ -1,33 +1,23 @@
 # Config file for automatic testing at travis-ci.org
-
 language: python
-  - "2.7"
-sudo: false
+python:
+  - 2.7
+  - 3.6
 before_install:
   - sudo apt-get -qq update
-  - sudo apt-get install -y build-essential git libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev
-  - sudo apt-get clean
-  - sudo apt-get autoclean
-install:
-  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes
-  - conda update -q conda
-  - conda clean --all
-  - conda install numpy=1.16.1
-  - conda install cython
-  - conda install swig
-  - pip install chaco scikit-image enable nose future  
-  - pip install optv
-  - pip install --user coveralls
-  - conda install conda-build
-  - conda build .
-  - conda install --use-local pyptv
-  - conda info -a
+  - sudo apt-get install -y build-essential 
+  - sudo apt-get install -y python-dev swig
+  - sudo apt-get -y install python-qt4-gl libx11-dev libpcre3 libpcre3-dev freeglut3-dev libgtk2.0-dev
+  - sudo apt-get -y install libgl1-mesa-glx libglu1-mesa-dev libgl1-mesa-dev mesa-common-dev 
 script:
+  - virtualenv --python=python venv
+  - source venv/bin/activate
+  - python -m pip install -U pip
+  - pip install -U wheel
+  - pip install numpy==1.16.1
+  - pip install optv==0.2.5
+  - pip install nose
+  - pip install scikit-image
+  - python setup.py install
   - cd tests
-  - nosetests -v
-after_success:
-  - coveralls
+  - nosetests --verbose

pyptv/calibration_gui.py

@@ -330,8 +330,8 @@ def __init__(self, active_path):
             self.n_cams = int(f.readline())
 
 
-        self.camera = [PlotWindow() for i in xrange(self.n_cams)]
-        for i in xrange(self.n_cams):
+        self.camera = [PlotWindow() for i in range(self.n_cams)]
+        for i in range(self.n_cams):
             self.camera[i].name = "Camera" + str(i + 1)
             self.camera[i].cameraN = i
             self.camera[i].py_rclick_delete = ptv.py_rclick_delete
@@ -431,7 +431,7 @@ def _button_showimg_fired(self):
         self.cpar, self.spar, self.vpar, self.track_par, self.tpar, \
         self.cals, self.epar = ptv.py_start_proc_c(self.n_cams)
 
-        self.tpar.read('parameters/detect_plate.par')
+        self.tpar.read(b'parameters/detect_plate.par')
 
         print(self.tpar.get_grey_thresholds())
 
@@ -447,7 +447,7 @@ def _button_showimg_fired(self):
                 print(self.MultiParams.plane_name[i])
 
             self.pass_raw_orient = True
-            self.status_text = "Multiplane calibration."
+            self.status_text = b"Multiplane calibration."
 
 
         # read calibration images
@@ -568,7 +568,7 @@ def _button_init_guess_fired(self):
         for i_cam in range(self.n_cams):
             cal = Calibration()
             tmp = self.cpar.get_cal_img_base_name(i_cam)
-            cal.from_file(tmp + '.ori', tmp + '.addpar')
+            cal.from_file(tmp + b'.ori', tmp + b'.addpar')
             self.cals.append(cal)
 
         for i_cam in range(self.n_cams):
@@ -779,7 +779,7 @@ def _button_fine_orient_fired(self):
                 # combined information
 
                 targs = TargetArray(len(all_detected))
-                for tix in xrange(len(all_detected)):
+                for tix in range(len(all_detected)):
                     targ = targs[tix]
                     det = all_detected[tix]
 
@@ -830,7 +830,7 @@ def _write_ori(self, i_cam):
         ori = self.calParams.img_ori[i_cam]
         addpar = ori.replace('ori', 'addpar')
         print("Saving:", ori, addpar)
-        self.cals[i_cam].write(ori, addpar)
+        self.cals[i_cam].write(ori.encode(), addpar.encode())
         if self.epar.Examine_Flag and not self.epar.Combine_Flag:
             self.save_point_sets(i_cam)
 
@@ -898,7 +898,7 @@ def reset_plots(self):
 
     def reset_show_images(self):
         for i,cam in enumerate(self.camera):
-            cam._plot.delplot(*cam._plot.plots.keys()[0:])
+            cam._plot.delplot(*list(cam._plot.plots.keys())[0:])
             cam._plot.overlays = []
             # self.camera[i]._plot_data.set_data('imagedata',self.ori_img[i].astype(np.byte))
             cam._plot_data.set_data('imagedata', self.cal_images[i].astype(np.byte))

pyptv/parameter_gui.py

@@ -909,12 +909,11 @@ def _reload(self):
         # read manual orientaion parameters
         manOriParams = par.ManOriParams(self.n_img, [], path=self.par_path)
         manOriParams.read()
-        nr = manOriParams.nr
 
 
         for i in range(self.n_img):
             for j in range(4): # 4 points per image
-                exec('self.img_{0}_p{1} = nr[{2}][{3}]'.format(i+1,j+1,i,j))
+                exec('self.img_{0}_p{1} = manOriParams.nr[{2}][{3}]'.format(i+1,j+1,i,j))
 
 
         # examine arameters

pyptv/ptv.py

@@ -30,34 +30,34 @@ def py_start_proc_c(n_cams):
 
     # Control parameters
     cpar = ControlParams(n_cams)
-    cpar.read_control_par('parameters/ptv.par')
+    cpar.read_control_par(b'parameters/ptv.par')
 
     # Sequence parameters
     spar = SequenceParams(num_cams=n_cams)
-    spar.read_sequence_par('parameters/sequence.par',n_cams)
+    spar.read_sequence_par(b'parameters/sequence.par',n_cams)
 
     # Volume parameters
     vpar = VolumeParams()
-    vpar.read_volume_par('parameters/criteria.par')
+    vpar.read_volume_par(b'parameters/criteria.par')
 
     # Tracking parameters
     track_par = TrackingParams()
-    track_par.read_track_par('parameters/track.par')
+    track_par.read_track_par(b'parameters/track.par')
 
     # Target parameters
     tpar = TargetParams(n_cams)
-    tpar.read('parameters/targ_rec.par')
+    tpar.read(b'parameters/targ_rec.par')
 
     # Examine parameters, multiplane (single plane vs combined calibration)
     epar= par.ExamineParams()
     epar.read()
 
     # Calibration parameters
     cals =[]
-    for i_cam in xrange(n_cams):
+    for i_cam in range(n_cams):
         cal = Calibration()
         tmp = cpar.get_cal_img_base_name(i_cam)
-        cal.from_file(tmp+'.ori', tmp+'.addpar')
+        cal.from_file(tmp + b'.ori', tmp + b'.addpar')
         cals.append(cal)
 
     return cpar, spar, vpar, track_par, tpar, cals, epar
@@ -116,7 +116,7 @@ def py_correspondences_proc_c(exp):
         exp.detections, exp.corrected, exp.cals, exp.vpar, exp.cpar)
 
     # Save targets only after they've been modified:
-    for i_cam in xrange(exp.n_cams):
+    for i_cam in range(exp.n_cams):
         exp.detections[i_cam].write(exp.spar.get_img_base_name(i_cam),frame)
 
     print("Frame " + str(frame) + " had " \
@@ -129,17 +129,17 @@ def py_determination_proc_c(n_cams, sorted_pos, sorted_corresp, corrected):
 
     # Control parameters
     cpar = ControlParams(n_cams)
-    cpar.read_control_par('parameters/ptv.par')
+    cpar.read_control_par(b'parameters/ptv.par')
 
     # Volume parameters
     vpar = VolumeParams()
-    vpar.read_volume_par('parameters/criteria.par')
+    vpar.read_volume_par(b'parameters/criteria.par')
 
     cals =[]
-    for i_cam in xrange(n_cams):
+    for i_cam in range(n_cams):
         cal = Calibration()
         tmp = cpar.get_cal_img_base_name(i_cam)
-        cal.from_file(tmp+'.ori', tmp+'.addpar')
+        cal.from_file(tmp + b'.ori', tmp + b'.addpar')
         cals.append(cal)
 
 
@@ -149,7 +149,7 @@ def py_determination_proc_c(n_cams, sorted_pos, sorted_corresp, corrected):
 
 
     flat = np.array([corrected[i].get_by_pnrs(sorted_corresp[i]) \
-                     for i in xrange(len(cals))])
+                     for i in range(len(cals))])
     pos, rcm = point_positions(
         flat.transpose(1,0,2), cpar, cals, vpar)
 
@@ -182,21 +182,22 @@ def py_sequence_loop(exp):
     Existing_Target = np.bool(pftVersionParams.Existing_Target)
 
     # sequence loop for all frames
-    for frame in xrange(spar.get_first(), spar.get_last()+1):
+    for frame in range(spar.get_first(), spar.get_last()+1):
         print("processing frame %d" % frame)
 
         detections = []
         corrected = []
-        for i_cam in xrange(n_cams):
+        for i_cam in range(n_cams):
             if Existing_Target:
                 targs = read_targets(spar.get_img_base_name(i_cam),frame)
             else:
-                imname = spar.get_img_base_name(i_cam) + str(frame)
+                imname = spar.get_img_base_name(i_cam) + str(frame).encode()
+                print(imname)
                 if not os.path.exists(imname):
                     print(os.path.abspath(os.path.curdir))
                     print('{0} does not exist'.format(imname))
 
-                img = imread(imname)
+                img = imread(imname.decode())
                 # time.sleep(.1) # I'm not sure we need it here
                 hp = simple_highpass(img, cpar)
                 targs = target_recognition(hp, tpar, i_cam, cpar)
@@ -216,7 +217,7 @@ def py_sequence_loop(exp):
             detections, corrected, cals, vpar, cpar)
 
         # Save targets only after they've been modified:
-        for i_cam in xrange(n_cams):
+        for i_cam in range(n_cams):
             detections[i_cam].write(spar.get_img_base_name(i_cam),frame)
 
 
@@ -228,7 +229,7 @@ def py_sequence_loop(exp):
         sorted_corresp = np.concatenate(sorted_corresp, axis=1)
 
         flat = np.array([corrected[i].get_by_pnrs(sorted_corresp[i]) \
-                         for i in xrange(len(cals))])
+                         for i in range(len(cals))])
         pos, rcm = point_positions(
             flat.transpose(1,0,2), cpar, cals, vpar)
 
@@ -243,7 +244,8 @@ def py_sequence_loop(exp):
             print_corresp = sorted_corresp
 
         # Save rt_is
-        rt_is = open(default_naming['corres']+'.'+str(frame), 'w')
+        print(default_naming['corres'])
+        rt_is = open(default_naming['corres']+b'.'+ str(frame).encode(), 'w')
         rt_is.write(str(pos.shape[0]) + '\n')
         for pix, pt in enumerate(pos):
             pt_args = (pix + 1,) + tuple(pt) + tuple(print_corresp[:,pix])
@@ -421,7 +423,7 @@ def py_multiplanecalibration(exp):
 		all_detected = np.vstack(all_detected)
 
 		targs = TargetArray(len(all_detected))
-		for tix in xrange(len(all_detected)):
+		for tix in range(len(all_detected)):
 			targ = targs[tix]
 			det = all_detected[tix]
 

pyptv/pyptv_batch.py

@@ -52,25 +52,25 @@ def run_batch(new_seq_first, new_seq_last):
 
     # Control parameters
     cpar = ControlParams(n_cams)
-    cpar.read_control_par('parameters/ptv.par')
+    cpar.read_control_par(b'parameters/ptv.par')
 
     # Sequence parameters
     spar = SequenceParams(num_cams=n_cams)
-    spar.read_sequence_par('parameters/sequence.par',n_cams)
+    spar.read_sequence_par(b'parameters/sequence.par',n_cams)
     spar.set_first(new_seq_first)
     spar.set_last(new_seq_last)
 
     # Volume parameters
     vpar = VolumeParams()
-    vpar.read_volume_par('parameters/criteria.par')
+    vpar.read_volume_par(b'parameters/criteria.par')
 
     # Tracking parameters
     track_par = TrackingParams()
-    track_par.read_track_par('parameters/track.par')
+    track_par.read_track_par(b'parameters/track.par')
 
     # Target parameters
     tpar = TargetParams()
-    tpar.read('parameters/targ_rec.par')
+    tpar.read(b'parameters/targ_rec.par')
 
     # 
 
@@ -80,7 +80,7 @@ def run_batch(new_seq_first, new_seq_last):
     for i_cam in range(n_cams):
         cal = Calibration()
         tmp = cpar.get_cal_img_base_name(i_cam)
-        cal.from_file(tmp+'.ori', tmp+'.addpar')
+        cal.from_file(tmp+b'.ori', tmp+b'.addpar')
         cals.append(cal)
 
 
@@ -165,7 +165,7 @@ def main(exp_path, first, last, repetitions=1):
 
     try:
         exp_path = os.path.abspath(exp_path)
-        print('exp_path= %s' % exp_path)
+        print('exp_path is %s' % exp_path)
         os.chdir(exp_path)
         print(os.getcwd())
     except:

pyptv/pyptv_gui.py

@@ -43,7 +43,7 @@
 
 # pyPTV specific imports
 import parameters as par
-from parameter_gui import Experiment, Paramset
+from parameter_gui import Experiment, Paramset, Calib_Params
 from calibration_gui import CalibrationGUI
 from directory_editor import DirectoryEditorDialog
 from quiverplot import QuiverPlot
@@ -369,7 +369,7 @@ def configure_cal_par(self, editor, object):
         print(len(experiment.paramsets))
         if paramset.c_params is None:
             # TODO: is it possible that control reaches here? If not, probably the if should be removed.
-            paramset.c_params = par.Calib_Params()
+            paramset.c_params = par.CalOriParams() # this is a very questionable line
         else:
             paramset.c_params._reload()
         paramset.c_params.edit_traits(kind='modal')
@@ -601,7 +601,7 @@ def sequence_action(self, info):
         """
 
         extern_sequence = info.object.plugins.sequence_alg
-        if extern_sequence != 'default':
+        if extern_sequence is not 'default':
             try:
                 # change to pyptv folder, look for tracking module
                 sys.path.append(software_path)
@@ -624,7 +624,7 @@ def track_no_disp_action(self, info):
         """ track_no_disp_action uses ptv.py_trackcorr_loop(..) binding to call tracking without display
         """
         extern_tracker = info.object.plugins.track_alg
-        if extern_tracker != 'default':
+        if extern_tracker is not 'default':
             try:
                 os.chdir(software_path)  # change to software path, to load tracking module
                 track = __import__(extern_tracker)  # import choosen tracker from software dir
@@ -1053,7 +1053,7 @@ def clear_plots(self, remove_background=True):
             index = None
 
         for i in range(len(self.camera_list)):
-            plot_list = self.camera_list[i]._plot.plots.keys()
+            plot_list = list(self.camera_list[i]._plot.plots.keys())
             # if not remove_background:
             #   index=None
             try:
@@ -1158,7 +1158,7 @@ def main():
     else:
         print(
             'Please provide an experimental directory as an input, fallback to a default\n')
-        exp_path = '../../2D_jet'
+        exp_path = '/Users/alex/Documents/OpenPTV/test_cavity'
 
     if not os.path.isdir(exp_path):
         raise OSError("Wrong experimental directory %s " % exp_path)

requirements.txt

@@ -1,6 +1,6 @@
-optv
 numpy==1.16.1
 scikit-image
 chaco
 enable
-future
+optv==0.2.5
+