see #59 checkbox for keeping memmap in caiman viewer modules

mesmerize/viewer/modules/batch_run_modules/CNMF.py

@@ -64,11 +64,12 @@ def run(batch_dir: str, UUID: str):
     except Exception as e:
         output.update({'status': 0, 'output_info': traceback.format_exc()})
 
-    for mf in glob(os.path.join(batch_dir, f'memmap-{UUID}*')):
-        try:
-            os.remove(mf)
-        except:
-            pass
+    if not input_params.get('keep_memmap', False):
+        for mf in glob(os.path.join(batch_dir, f'memmap-{UUID}*')):
+            try:
+                os.remove(mf)
+            except:
+                pass
 
     end_time = time()
     proc_time = (end_time - start_time) / 60

mesmerize/viewer/modules/batch_run_modules/CNMFE.py

@@ -207,11 +207,12 @@ def run(batch_dir: str, UUID: str):
 
     dview.terminate()
 
-    for mf in glob(batch_dir + '/memmap-*'):
-        try:
-            os.remove(mf)
-        except: # Windows doesn't like removing the memmaps
-            pass
+    if not input_params.get('keep_memmap', False):
+        for mf in glob(batch_dir + '/memmap-*'):
+            try:
+                os.remove(mf)
+            except: # Windows doesn't like removing the memmaps
+                pass
 
     end_time = time()
     processing_time = (end_time - start_time) / 60

mesmerize/viewer/modules/batch_run_modules/caiman_motion_correction.py

@@ -80,7 +80,7 @@ def run_single(batch_dir, UUID, output):
 
     fname = [file_path + '_input.tiff']
     # TODO: Should just unpack the input params as kwargs
-    input_params = pickle.load(open(file_path + '.params', 'rb'))
+    input_params: dict = pickle.load(open(file_path + '.params', 'rb'))
     mc_kwargs = input_params['mc_kwargs']
 
     splits_rig = n_processes
@@ -130,11 +130,12 @@ def run_single(batch_dir, UUID, output):
 
     output.update({'status': 1, 'bord_px': int(bord_px_els)})
 
-    for mf in glob(os.path.join(batch_dir, UUID + '*.mmap')):
-        try:
-            os.remove(mf)
-        except:
-            pass
+    if not input_params.get('keep_memmap', False):
+        for mf in glob(os.path.join(batch_dir, UUID + '*.mmap')):
+            try:
+                os.remove(mf)
+            except:
+                pass
 
     dview.terminate()
 

mesmerize/viewer/modules/caiman_motion_correction.py

@@ -149,6 +149,8 @@ def get_params(self, group_params: bool = False) -> dict:
         else:
             d.update({**mc_params})
 
+        d['keep_memmap'] = self.ui.checkBoxKeepMemmap.isChecked()
+
         return d
 
     def add_to_batch_elas_corr(self):

mesmerize/viewer/modules/cnmf.py

@@ -121,7 +121,8 @@ def get_params(self, *args, group_params: bool = False) -> dict:
                 'item_name': self.ui.lineEdName.text(),
                 'refit': self.ui.checkBoxRefit.isChecked(),
                 'border_pix': bord_px,
-                'is_3d': is_3d
+                'is_3d': is_3d,
+                'keep_memmap': self.ui.checkBoxKeepMemmap.isChecked()
             }
 
         # Group the kwargs of the two parts seperately

mesmerize/viewer/modules/cnmfe.py

@@ -168,6 +168,8 @@ def get_params(self, item_type: str, group_params: bool = False) -> dict:
         else:
             raise ValueError("Must specify argument `item_type` as either 'corr_pnr' or 'cnmfe'")
 
+        d['keep_memmap'] = self.ui.checkBoxKeepMemmap.isChecked()
+
         return d
 
     def add_to_batch_corr_pnr(self, params: dict = None) -> UUID:

mesmerize/viewer/modules/ui_files/caiman_motion_correction.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>287</width>
-    <height>842</height>
+    <width>279</width>
+    <height>869</height>
    </rect>
   </property>
   <property name="floating">
@@ -507,6 +507,13 @@ Use single quotes for strings, do not use double quotes.</string>
       </item>
      </layout>
     </item>
+    <item>
+     <widget class="QCheckBox" name="checkBoxKeepMemmap">
+      <property name="text">
+       <string>Keep memmap</string>
+      </property>
+     </widget>
+    </item>
     <item>
      <layout class="QHBoxLayout" name="horizontalLayout_20">
       <item>
@@ -609,8 +616,11 @@ Use single quotes for strings, do not use double quotes.</string>
   <tabstop>sliderOverlaps</tabstop>
   <tabstop>btnShowQuilt</tabstop>
   <tabstop>spinboxUpsample</tabstop>
+  <tabstop>checkBoxKeepMemmap</tabstop>
   <tabstop>lineEditNameElastic</tabstop>
   <tabstop>btnAddToBatchElastic</tabstop>
+  <tabstop>comboBoxProjectionsOption</tabstop>
+  <tabstop>pushButtonViewProjections</tabstop>
  </tabstops>
  <resources/>
  <connections>

mesmerize/viewer/modules/ui_files/cnmf_pytemplate.ui

@@ -506,7 +506,7 @@ Use single quotes for strings, do not use double quotes.</string>
          <string/>
         </property>
         <property name="title">
-         <string>Use additional CNMF params</string>
+         <string>&amp;Use additional CNMF params</string>
         </property>
         <property name="checkable">
          <bool>true</bool>
@@ -800,6 +800,13 @@ Use single quotes for strings, do not use double quotes</string>
         </item>
        </layout>
       </item>
+      <item>
+       <widget class="QCheckBox" name="checkBoxKeepMemmap">
+        <property name="text">
+         <string>Keep memmap</string>
+        </property>
+       </widget>
+      </item>
       <item>
        <layout class="QHBoxLayout" name="horizontalLayout_11">
         <item>
@@ -849,6 +856,7 @@ Use single quotes for strings, do not use double quotes</string>
   <tabstop>groupBox_eval_kwargs</tabstop>
   <tabstop>plainTextEdit_eval_kwargs</tabstop>
   <tabstop>checkBoxRefit</tabstop>
+  <tabstop>checkBoxKeepMemmap</tabstop>
   <tabstop>lineEdName</tabstop>
   <tabstop>btnAddToBatchCNMF</tabstop>
  </tabstops>

mesmerize/viewer/modules/ui_files/cnmfe_pytemplate.ui

@@ -865,6 +865,13 @@ Use single quotes for strings, do not use double quotes</string>
         </layout>
        </widget>
       </item>
+      <item>
+       <widget class="QCheckBox" name="checkBoxKeepMemmap">
+        <property name="text">
+         <string>Keep memmap</string>
+        </property>
+       </widget>
+      </item>
       <item>
        <layout class="QHBoxLayout" name="horizontalLayout_11">
         <item>
@@ -927,6 +934,7 @@ Use single quotes for strings, do not use double quotes</string>
   <tabstop>doubleSpinBoxDecayTime</tabstop>
   <tabstop>groupBox_eval_kwargs</tabstop>
   <tabstop>plainTextEdit_eval_kwargs</tabstop>
+  <tabstop>checkBoxKeepMemmap</tabstop>
   <tabstop>lineEdName</tabstop>
   <tabstop>btnAddToBatchCNMFE</tabstop>
  </tabstops>