Merge pull request #35 from logicvay2010/isonet

Fix new issues

bin/mask_one.py

@@ -8,7 +8,7 @@
 from TomoNet.util.io import log
 from TomoNet.util.searchParam import SearchParam 
 
-def make_mask_one(tomo_path, mask_name, mask_boundary = None, side = 5, density_percentage=50.0, std_percentage=50.0, surface=None):
+def make_mask_one(tomo_path, mask_name, mask_boundary = None, side = 5, density_percentage=50.0, std_percentage=50.0, surface=None, logger=None):
 
         with mrcfile.open(tomo_path, permissive=True) as n:
             header_input = n.header
@@ -33,7 +33,7 @@ def make_mask_one(tomo_path, mask_name, mask_boundary = None, side = 5, density_
 
         if mask_boundary is not None:
             from TomoNet.util.filter import boundary_mask
-            mask3 = boundary_mask(bintomo, mask_boundary, logger=self.logger)
+            mask3 = boundary_mask(bintomo, mask_boundary, logger=logger)
             out_mask_bin = np.multiply(out_mask_bin, mask3)
 
         if (surface is not None) and surface < 1:
@@ -92,6 +92,6 @@ def make_mask_one(tomo_path, mask_name, mask_boundary = None, side = 5, density_
 
     make_mask_one(mask_params.tomo_file, mask_params.mask_out_name, mask_params.mask_boundary, 
                   mask_params.side, mask_params.density_percentage, 
-                  mask_params.std_percentage, mask_params.surface)
+                  mask_params.std_percentage, mask_params.surface, logger=logger)
 
     log(logger, 'time consumed: {:10.4f} s'.format(time.time()-t1))

process/bash_expand.py

@@ -27,17 +27,19 @@ def run(self):
             #subprocess.check_output(cmd, shell=True)
 
             self.p = QProcess()
-
             self.p.start(cmd)
-            res = self.p.waitForFinished(86400)
-
-            try:
-                if cmd.split()[4] == '0':
-                    self.logger.info("Finish generating a new final folder for {}".format(cmd.split()[3]))
-                else:
-                    self.logger.info("Finish expand {} for {} rounds".format(cmd.split()[3],cmd.split()[4]))
-            except:
-                pass
+            res = self.p.waitForFinished(8.64e7)
+
+            if res:
+                try:
+                    if cmd.split()[4] == '0':
+                        self.logger.info("Finish generating a new final folder for {}".format(cmd.split()[3]))
+                    else:
+                        self.logger.info("Finish expand {} for {} rounds".format(cmd.split()[3],cmd.split()[4]))
+                except:
+                    pass
+            else:
+                self.logger.error("Expand failed for {}".format(cmd.split()[3]))
             try:
                 self.kill_process()
             except:

process/bash_isonet_deconv.py

@@ -78,7 +78,7 @@ def run(self):
                     self.logger.info("Running deconv command: {}".format(cmd))
                     self.p = QProcess()
                     self.p.start(cmd)
-                    res = self.p.waitForFinished(86400)
+                    res = self.p.waitForFinished(60000*30)
                     # deconv_one(it.rlnMicrographName, deconv_tomo_name, self.isonet_folder, voltage=self.voltage, cs=self.cs, defocus=it.rlnDefocus/10000.0, \
                     #         pixel_size=it.rlnPixelSize, snrfalloff=it.rlnSnrFalloff, deconvstrength=it.rlnDeconvStrength, \
                     #             highpassnyquist=self.highpassnyquist, chunk_size=self.chunk_size, overlap_rate=self.overlap_rate, ncpu=self.ncpu, logger=self.logger)

process/bash_isonet_generate_mask.py

@@ -92,7 +92,7 @@ def run(self):
                             self.logger.info("Running mask generation command: {}".format(cmd))
                             self.p = QProcess()
                             self.p.start(cmd)
-                            res = self.p.waitForFinished(86400)
+                            res = self.p.waitForFinished(60000*30)
 
                             try:
                                 self.p.terminate()

process/bash_isonet_predict_network.py

@@ -14,7 +14,7 @@ def run(self):
         self.p = QProcess()
 
         self.p.start(self.cmd)
-        res = self.p.waitForFinished(86400)
+        res = self.p.waitForFinished(8.64e7)
         #self.p.finished.connect(self.kill_process)
 
     def stop_process(self):

process/bash_isonet_train_network.py

@@ -14,7 +14,7 @@ def run(self):
         self.p = QProcess()
 
         self.p.start(self.cmd)
-        res = self.p.waitForFinished(86400)
+        res = self.p.waitForFinished(8.64e7*3)
         #self.p.finished.connect(self.kill_process)
 
     def stop_process(self):

process/bash_predict_network.py

@@ -74,7 +74,7 @@ def run(self):
                 self.p = QProcess()
                 self.p.start(cmd)
                 #self.logger.info("PID {}".format(self.p.pid()))
-                res = self.p.waitForFinished(86400)
+                res = self.p.waitForFinished(8.64e7)
 
                 try:
                     self.p.terminate() 

process/bash_train_network.py

@@ -58,15 +58,15 @@ def run(self):
             self.p = QProcess()
             self.p.start(cmd)
             #self.logger.info("PID {}".format(self.p.pid()))
-            res = self.p.waitForFinished(86400)
+            res = self.p.waitForFinished(8.64e7*3)
             #subprocess.run(cmd, shell=True, encoding="utf-8", stdout=subprocess.PIPE)
 
             # with open("{}/train_params.json".format(self.d['result_folder_train']), 'w') as fp:
             #     json.dump(self.d, fp, indent=2, default=int)
 
             #clean process 
             try:
-                self.p.terminate() 
+                self.p.terminate(8.64e7*3) 
                 #self.p.close()
             except:
                 pass