Merge 3188a31 into 105cbf1

testbeam_analysis/examples/telescope_time_reference.py

@@ -93,6 +93,7 @@ def run_analysis():
     # Merge the cluster tables to one merged table aligned at the event number
     dut_alignment.merge_cluster_data(input_cluster_files=input_cluster_files,
                                      output_merged_file=os.path.join(output_folder, 'Merged.h5'),
+                                     n_pixels=n_pixels,
                                      pixel_size=pixel_size)
 
     # Apply the prealignment to the merged cluster table to create tracklets

testbeam_analysis/gui/tab_widgets/files_tab.py

@@ -385,10 +385,12 @@ def check_data(self):
                         else:
                             missing.append(req)
                     if len(missing) != 0:
-                        self.incompatible_data[i] = 'Error! Data does not contain field(s):\n' + ', '.join(missing)
+                        self.incompatible_data[i] = 'Data does not contain field(s):\n' + ', '.join(missing)
+                    if f.root.Hits.shape[0] == 0:
+                        self.incompatible_data[i] = 'Hit data is empty!'
 
                 except tb.exceptions.NoSuchNodeError:
-                    self.incompatible_data[i] = 'No Hits! Existing nodes:\n' + ', '.join([node.name for node in f.root])
+                    self.incompatible_data[i] = 'No Hits node! Found nodes:\n' + ', '.join([node.name for node in f.root])
 
         font = QtGui.QFont()
         font.setBold(True)

testbeam_analysis/tools/plot_utils.py

@@ -544,7 +544,10 @@ def fit_data():
         global offset
         global fit
         global fit_fn
-        fit, _ = curve_fit(testbeam_analysis.tools.analysis_utils.linear, x[selected_data], mean_fitted[selected_data])  # Fit straight line
+        try:
+            fit, _ = curve_fit(testbeam_analysis.tools.analysis_utils.linear, x[selected_data], mean_fitted[selected_data])  # Fit straight line
+        except TypeError:  # if number of points < 2
+            raise RuntimeError('Cannot find any correlation, please check data!')
         fit_fn = np.poly1d(fit[::-1])
         offset = fit_fn(x) - mean_fitted  # Calculate straight line fit offset
 
@@ -592,13 +595,13 @@ def fit_data():
         ax2.legend(lines + lines2, labels + labels2, loc=0)
         ax.grid()
         # Setup interactive sliders/buttons
-        ax_offset = plt.axes([0.410, 0.04, 0.2, 0.02], axisbg='white')
-        ax_error = plt.axes([0.410, 0.01, 0.2, 0.02], axisbg='white')
-        ax_left_limit = plt.axes([0.125, 0.04, 0.2, 0.02], axisbg='white')
-        ax_right_limit = plt.axes([0.125, 0.01, 0.2, 0.02], axisbg='white')
-        ax_button_auto = plt.axes([0.670, 0.01, 0.06, 0.05], axisbg='black')
-        ax_button_refit = plt.axes([0.735, 0.01, 0.08, 0.05], axisbg='black')
-        ax_button_ok = plt.axes([0.82, 0.01, 0.08, 0.05], axisbg='black')
+        ax_offset = plt.axes([0.410, 0.04, 0.2, 0.02], facecolor='white')
+        ax_error = plt.axes([0.410, 0.01, 0.2, 0.02], facecolor='white')
+        ax_left_limit = plt.axes([0.125, 0.04, 0.2, 0.02], facecolor='white')
+        ax_right_limit = plt.axes([0.125, 0.01, 0.2, 0.02], facecolor='white')
+        ax_button_auto = plt.axes([0.670, 0.01, 0.06, 0.05], facecolor='black')
+        ax_button_refit = plt.axes([0.735, 0.01, 0.08, 0.05], facecolor='black')
+        ax_button_ok = plt.axes([0.82, 0.01, 0.08, 0.05], facecolor='black')
         # Create widgets
         offset_slider = Slider(ax=ax_offset, label='Offset limit', valmin=0.0, valmax=offset_limit, valinit=offset_limit, closedmin=True, closedmax=True)
         error_slider = Slider(ax=ax_error, label='Error limit', valmin=0.0, valmax=error_limit * 10.0, valinit=error_limit * 10.0, closedmin=True, closedmax=True)

testbeam_analysis/tools/smc.py

@@ -103,18 +103,15 @@ def __init__(self, table_file_in, file_out,
             raise NotImplementedError('Data alignment is only supported '
                                       'on event_number')
 
-
-
         # Get the table node name
         with tb.open_file(table_file_in) as in_file:
             if not table:  # Find the table node
-                tables = in_file.list_nodes('/',classname='Table') # get all nodes of type 'table'
-                if  len(tables) == 1: # if there is only one table, take this one
+                tables = in_file.list_nodes('/', classname='Table')  # get all nodes of type 'table'
+                if len(tables) == 1:  # if there is only one table, take this one
                     self.node_name = tables[0].name
-                else:  #  Multiple tables
-                    raise RuntimeError('No table node defined and '
-                                       'multiple table nodes found in file')
-            elif isinstance(table,(list,tuple,set)):  # possible names
+                else:  # Multiple tables
+                    raise RuntimeError('No table node defined and multiple table nodes found in file')
+            elif isinstance(table, (list, tuple, set)):  # possible names
                 self.node_name = None
                 for node_cand in table:
                     try:
@@ -123,8 +120,7 @@ def __init__(self, table_file_in, file_out,
                     except tb.NoSuchNodeError:
                         pass
                 if not self.node_name:
-                    raise RuntimeError(
-                        'No table nodes with names %s found', str(table))
+                    raise RuntimeError('No table nodes with names %s found', str(table))
             else:  # string
                 self.node_name = table
 
@@ -155,6 +151,7 @@ def _split(self):
         assert len(self.start_i) == len(self.stop_i)
 
     def _map(self):
+        chunk_size_per_core = int(self.chunk_size / self.n_cores)
         if self.n_cores == 1:
             self.tmp_files = [self._work(self.table_file_in,
                                          self.node_name,
@@ -163,7 +160,7 @@ def _map(self):
                                          self.node_desc,
                                          self.start_i[0],
                                          self.stop_i[0],
-                                         self.chunk_size)]
+                                         chunk_size_per_core)]
         else:
             # Run function in parallel
             pool = Pool(self.n_cores)
@@ -179,7 +176,7 @@ def _map(self):
                                   node_desc=self.node_desc,
                                   start_i=self.start_i[i],
                                   stop_i=self.stop_i[i],
-                                  chunk_size=self.chunk_size
+                                  chunk_size=chunk_size_per_core
                                   )
                 jobs.append(job)
 
@@ -204,7 +201,7 @@ def _work(self, table_file_in, node_name, func, func_kwargs,
         with tb.open_file(table_file_in, 'r') as in_file:
             node = in_file.get_node(in_file.root, node_name)
 
-            output_file = tempfile.NamedTemporaryFile(delete=False)
+            output_file = tempfile.NamedTemporaryFile(delete=False, dir=os.getcwd())
             with tb.open_file(output_file.name, 'w') as out_file:
                 # Create result table with specified data format
                 # From given pytables tables description