Merge branch 'dev' into main

dashUI/convert.py

@@ -27,13 +27,13 @@ module = 'convert'
 inputtypes = [
     {'label': 'SBEMImage', 'value': 'SBEM'},
     {'label': 'SerialEM Montage', 'value': 'SerialEM'},
-    # {'label': 'Image stack - FIB/SEM', 'value': 'FIBSEM'},
+    {'label': 'Image stack - FIB/SEM', 'value': 'tifstack'},
 ]
 
 inputmodules = [
     'inputtypes.sbem_conv',
     'inputtypes.serialem_conv',
-    # 'inputtypes.tifstack_conv'
+    'inputtypes.tifstack_conv'
 ]
 
 main = html.Div(children=[html.H3("Import volume EM datasets - Choose type:", id='conv_head'),

dashUI/inputtypes/tifstack_conv.py

@@ -59,6 +59,27 @@ pathbrowse = pages.path_browse(label)
 
 page1 = [directory_sel, pathbrowse, html.Div(store)]
 
+
+voxsz = html.Div(children=[html.H4("Resolution values"),
+                           "x/y (isotropic): ",
+                           dcc.Input(id={'component': 'xy_px_input', 'module': label}, type="number",
+                                     debounce=True,
+                                     value=10.0,
+                                     persistence=True),
+                           " nm",
+                           html.Br(),html.Br(),
+                            "z (milling step): ",
+                           dcc.Input(id={'component': 'z_px_input', 'module': label}, type="number",
+                                     debounce=True,
+                                     value=10.0,
+                                     persistence=True),
+                           " nm",
+                           ]
+                 )
+
+page1.append(voxsz)
+
+
 # # ===============================================
 #  RENDER STACK SELECTOR
 
@@ -152,10 +173,12 @@ page2.append(collapse_stdout)
                ],
               [State({'component': 'project_dd', 'module': label}, 'value'),
                State(label + 'compute_sel', 'value'),
+               State({'component': 'xy_px_input', 'module': label}, 'value'),
+               State({'component': 'z_px_input', 'module': label}, 'value'),
                State({'component': 'store_run_status', 'module': label}, 'data'),
                State({'component': 'store_render_launch', 'module': label}, 'data')],
               prevent_initial_call=True)
-def tifstack_conv_gobutton(stack_sel, in_dir, click, proj_dd_sel, compute_sel, run_state, outstore):
+def tifstack_conv_gobutton(stack_sel, in_dir, click, proj_dd_sel, compute_sel, pxs, zwidth, run_state, outstore):
     ctx = dash.callback_context
     trigger = ctx.triggered[0]['prop_id'].split('.')[0].partition(label)[2]
     but_disabled = True
@@ -184,27 +207,33 @@ def tifstack_conv_gobutton(stack_sel, in_dir, click, proj_dd_sel, compute_sel, r
         with open(os.path.join(params.json_template_dir, 'SBEMImage_importer.json'), 'r') as f:
             run_params.update(json.load(f))
 
-        run_params['image_file'] = in_dir
+        run_params['image_directory'] = in_dir
         run_params['stack'] = stack_sel
 
+        vox_sz = [pxs/1000] * 2
+        vox_sz.append(zwidth/1000)
+
+        run_params['pxs'] = vox_sz
+
+
         with open(param_file, 'w') as f:
             json.dump(run_params, f, indent=4)
 
-        log_file = params.render_log_dir + '/' + 'serialem_conv_' + run_prefix
+        log_file = params.render_log_dir + '/' + 'tifstack_conv_' + run_prefix
         err_file = log_file + '.err'
         log_file += '.log'
 
         # launch
         # -----------------------
 
-        sbem_conv_p = launch_jobs.run(target=compute_sel,
+        tif_conv_p = launch_jobs.run(target=compute_sel,
                                       pyscript=params.rendermodules_dir +
-                                               '/dataimport/generate_EM_tilespecs_from_SerialEMmontage.py',
+                                               '/dataimport/generate_EM_tilespecs_from_TIFStack.py',
                                       jsonfile=param_file, run_args=None, logfile=log_file, errfile=err_file)
 
         run_state['status'] = 'running'
-        run_state['id'] = sbem_conv_p
-        run_state['type'] = launch_jobs.runtype(comp_sel)
+        run_state['id'] = tif_conv_p
+        run_state['type'] = launch_jobs.runtype(compute_sel)
         run_state['logfile'] = log_file
 
     else:
@@ -220,7 +249,7 @@ def tifstack_conv_gobutton(stack_sel, in_dir, click, proj_dd_sel, compute_sel, r
             run_state['status'] = 'wait'
             popup = 'Wrong characters in input directory path. Please fix!'
 
-        elif os.path.isfile(in_dir):
+        elif os.path.isdir(in_dir):
             # print(in_dir)
             if any([stack_sel == 'newstack', proj_dd_sel == 'newproj']):
                 if not (run_state['status'] == 'running'):