From 90933729585d49aecb96f3c179b5d55c5af0810b Mon Sep 17 00:00:00 2001
From: Gijs Schot <gijsschot@gmail.com>
Date: Mon, 11 Jan 2021 14:34:23 +0100
Subject: [PATCH] Small changes to GUI: added extra parameter to
 motioncorretion. Changed size to radius in extract candidates. and removed a
 check write in writeAlignedProjections

---
 gui/frameDataTransfer.py                  | 7 ++++++-
 gui/frameParticlePicking.py               | 4 ++--
 gui/guiStructures.py                      | 3 ++-
 reconstruction/writeAlignedProjections.py | 2 --
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/gui/frameDataTransfer.py b/gui/frameDataTransfer.py
index 67673c4a..cd1e4b96 100755
--- a/gui/frameDataTransfer.py
+++ b/gui/frameDataTransfer.py
@@ -179,6 +179,11 @@ def __init__(self, parent=None):
         self.activeProcesses = {}
         self.workerID = 0
         self.threadPool = self.parent().threadPool
+        self.progressBarCounters = {}
+        self.progressBars = {}
+        self.queueEvents = self.parent().qEvents
+        self.localqID = {}
+        self.activeProcesses = {}
 
         self.widgets['pytomPath'] = QLineEdit()
         self.widgets['pytomPath'].setText(self.parent().pytompath)
@@ -509,7 +514,7 @@ def createMotioncorGroup(self,mode='v01_single_'):
                                                       id='MotionCorrection')
         paramsCmd = [self.motioncor_folder, mode + 'fileTypeCapitalized', mode + 'folder_nanographs',
                      self.motioncor_folder, mode + 'gainFileFlag', mode + 'patchSizeFlag', mode + 'ftBinFlag',
-                     mode + 'gpuIdFlag', templateMotionCorrection]
+                     mode + 'gpuIdFlag', mode + 'filetype_nanographs', templateMotionCorrection]
 
         self.insert_gen_text_exe(parent, mode, paramsCmd=paramsCmd, exefilename=execfilename, paramsSbatch=paramsSbatch,
                                  cs=3, queue=True)
diff --git a/gui/frameParticlePicking.py b/gui/frameParticlePicking.py
index a3e9e7fc..c784aa20 100755
--- a/gui/frameParticlePicking.py
+++ b/gui/frameParticlePicking.py
@@ -606,7 +606,7 @@ def populate_batch_extract_cand(self,id='tab23'):
             print('\n\nPlease select at least one job file template and mask file.\n\n')
             return
 
-        headers = ["Job name", "Extract", "File Name Particle List", "Ouput Dir Subtomograms", "Size (px)",
+        headers = ["Job name", "Extract", "File Name Particle List", "Ouput Dir Subtomograms", "Radius (px)",
                    "# Candidates", 'Min. Score', '']
         types = ['txt', 'checkbox', 'lineedit', 'lineedit', 'lineedit', 'lineedit', 'lineedit', 'txt']
         sizes = [0, 0, 80, 150, 0, 0, 0, 0]
@@ -615,7 +615,7 @@ def populate_batch_extract_cand(self,id='tab23'):
                    'Select if you want to extract particles using this job file.',
                    'File name of particle list in which a number of candidates are written.',
                    'Prefix indicating in which folder particles will be saved when subtomograms are extracted',
-                   'Particle Size in pixels',
+                   'Radius of Particle of interest in pixels',
                    'Number of candidates extracted from tomogram.',
                    'Minimum cross-correlation coefficient for a particle to be selected.']
 
diff --git a/gui/guiStructures.py b/gui/guiStructures.py
index c4dfb6c7..158c2c69 100755
--- a/gui/guiStructures.py
+++ b/gui/guiStructures.py
@@ -962,7 +962,8 @@ def exe_action(self, params):
                 #     time.sleep(1)
                 # self.popup_messagebox('Info', 'Local Job Finished', f'Finished Job {ID}')
                 # os.system('sh {}'.format(params[0]))
-        except:
+        except Exception as e:
+            print(e)
             print ('Please check your input parameters. They might be incomplete.')
     '''
     def getLocalID(self):
diff --git a/reconstruction/writeAlignedProjections.py b/reconstruction/writeAlignedProjections.py
index ce39fce2..0d304168 100755
--- a/reconstruction/writeAlignedProjections.py
+++ b/reconstruction/writeAlignedProjections.py
@@ -154,9 +154,7 @@ def writeAlignedProjections(TiltSeries_, weighting=None,
 
 
             # 4 -- Rotate
-            print(transX, transY)
             image = general_transform2d(v=image, rot=rot, shift=[transX,transY], scale=mag, order=[2, 1, 0], crop=True)
-            image.write(f'resized_{ii}.em')
 
             # 5 -- Optional Low Pass Filter
             if lowpassFilter: