Merge branch 'release-1.1.3'

FlowCal/__init__.py

@@ -6,7 +6,7 @@
 # Versions should comply with PEP440.  For a discussion on single-sourcing
 # the version across setup.py and the project code, see
 # https://packaging.python.org/en/latest/single_source_version.html
-__version__ = '1.1.2'
+__version__ = '1.1.3'
 
 import io
 import excel_ui

FlowCal/excel_ui.py

@@ -380,14 +380,17 @@ def process_beads_table(beads_table,
                     beads_sample_gated,
                     channels=sc_channels)
             # Density gating
-            beads_sample_gated, __, gate_contour = FlowCal.gate.density2d(
-                data=beads_sample_gated,
-                channels=sc_channels,
-                gate_fraction=beads_row['Gate Fraction'],
-                xscale='logicle',
-                yscale='logicle',
-                sigma=5.,
-                full_output=True)
+            try:
+                beads_sample_gated, __, gate_contour = FlowCal.gate.density2d(
+                    data=beads_sample_gated,
+                    channels=sc_channels,
+                    gate_fraction=beads_row['Gate Fraction'],
+                    xscale='logicle',
+                    yscale='logicle',
+                    sigma=5.,
+                    full_output=True)
+            except ValueError as ve:
+                raise ExcelUIException(ve.message)
 
             # Plot forward/side scatter density plot and fluorescence histograms
             if plot:
@@ -782,13 +785,16 @@ def process_samples_table(samples_table,
                     sample_gated,
                     sc_channels + report_channels)
             # Density gating
-            sample_gated, __, gate_contour = FlowCal.gate.density2d(
-                data=sample_gated,
-                channels=sc_channels,
-                gate_fraction=sample_row['Gate Fraction'],
-                xscale='logicle',
-                yscale='logicle',
-                full_output=True)
+            try:
+                sample_gated, __, gate_contour = FlowCal.gate.density2d(
+                    data=sample_gated,
+                    channels=sc_channels,
+                    gate_fraction=sample_row['Gate Fraction'],
+                    xscale='logicle',
+                    yscale='logicle',
+                    full_output=True)
+            except ValueError as ve:
+                raise ExcelUIException(ve.message)
 
             # Plot forward/side scatter density plot and fluorescence histograms
             if plot:
@@ -1311,7 +1317,11 @@ def show_open_file_dialog(filetypes):
 
     return filename
 
-def run(input_path=None, output_path=None, verbose=True, plot=True):
+def run(input_path=None,
+        output_path=None,
+        verbose=True,
+        plot=True,
+        hist_sheet=False):
     """
     Run the MS Excel User Interface.
 
@@ -1324,11 +1334,12 @@ def run(input_path=None, output_path=None, verbose=True, plot=True):
      4. Generate statistics for each bead sample.
      5. Process all the cell samples in the Samples table.
      6. Generate statistics for each sample.
-     7. Generate a histogram table for each fluorescent channel specified
-        for each sample.
+     7. If requested, generate a histogram table for each fluorescent
+        channel specified for each sample.
      8. Generate a table with run time, date, FlowCal version, among
         others.
-     9. Save statistics and histograms in an output Excel file.
+     9. Save statistics and (if requested) histograms in an output Excel
+        file.
 
     Parameters
     ----------
@@ -1344,6 +1355,9 @@ def run(input_path=None, output_path=None, verbose=True, plot=True):
     plot : bool, optional
         Whether to generate and save density/histogram plots of each
         sample, and each beads sample.
+    hist_sheet : bool, optional
+        Whether to generate a sheet in the output Excel file specifying
+        histogram bin information.
 
     """
 
@@ -1406,9 +1420,10 @@ def run(input_path=None, output_path=None, verbose=True, plot=True):
     add_samples_stats(samples_table, samples)
 
     # Generate histograms
-    if verbose:
-        print("Generating histograms table...")
-    histograms_table = generate_histograms_table(samples_table, samples)
+    if hist_sheet:
+        if verbose:
+            print("Generating histograms table...")
+        histograms_table = generate_histograms_table(samples_table, samples)
 
     # Generate about table
     about_table = generate_about_table({'Input file path': input_path})
@@ -1418,7 +1433,8 @@ def run(input_path=None, output_path=None, verbose=True, plot=True):
     table_list.append(('Instruments', instruments_table))
     table_list.append(('Beads', beads_table))
     table_list.append(('Samples', samples_table))
-    table_list.append(('Histograms', histograms_table))
+    if hist_sheet:
+        table_list.append(('Histograms', histograms_table))
     table_list.append(('About Analysis', about_table))
 
     # Write output excel file
@@ -1459,10 +1475,16 @@ def run(input_path=None, output_path=None, verbose=True, plot=True):
         "--plot",
         action="store_true",
         help="generate and save density plots/histograms of beads and samples")
+    parser.add_argument(
+        "-H",
+        "--histogram-sheet",
+        action="store_true",
+        help="generate sheet in output Excel file specifying histogram bins")
     args = parser.parse_args()
 
     # Run Excel UI
     run(input_path=args.inputpath,
         output_path=args.outputpath,
         verbose=args.verbose,
-        plot=args.plot)
+        plot=args.plot,
+        hist_sheet=args.histogram_sheet)

FlowCal/gate.py

@@ -284,7 +284,8 @@ def density2d(data,
             bin edges. Note that None is not allowed if ``data.hist_bins``
             does not exist.
     gate_fraction : float, optional
-        Fraction of events to retain after gating.
+        Fraction of events to retain after gating. Should be between 0 and
+        1, inclusive.
     xscale : str, optional
         Scale of the bins generated for the x axis, either ``linear``,
         ``log``, or ``logicle``. `xscale` is ignored in `bins` is an array
@@ -349,11 +350,15 @@ def density2d(data,
 
     # Extract channels in which to gate
     if len(channels) != 2:
-        raise ValueError('2 channels should be specified.')
+        raise ValueError('2 channels should be specified')
     data_ch = data[:,channels]
     if data_ch.ndim == 1:
         data_ch = data_ch.reshape((-1,1))
 
+    # Check gating fraction
+    if gate_fraction < 0 or gate_fraction > 1:
+        raise ValueError('gate fraction should be between 0 and 1, inclusive')
+
     # Check dimensions
     if data_ch.ndim < 2:
         raise ValueError('data should have at least 2 dimensions')

FlowCal/plot.py

@@ -751,12 +751,16 @@ def hist1d(data_list,
         data_list = [data_list]
 
     # Default colors
-    if histtype == 'stepfilled' and edgecolor is None and facecolor is None:
-        facecolor = [cmap_default(i)
-                     for i in np.linspace(0, 1, len(data_list))]
-    elif histtype == 'step' and edgecolor is None and facecolor is None:
-        edgecolor = [cmap_default(i)
-                     for i in np.linspace(0, 1, len(data_list))]
+    if histtype == 'stepfilled':
+        if facecolor is None:
+            facecolor = [cmap_default(i)
+                         for i in np.linspace(0, 1, len(data_list))]
+        if edgecolor is None:
+            edgecolor = ['black']*len(data_list)
+    elif histtype == 'step':
+        if edgecolor is None:
+            edgecolor = [cmap_default(i)
+                         for i in np.linspace(0, 1, len(data_list))]
 
     # Convert colors to lists if necessary
     if not isinstance(edgecolor, list):

Run FlowCal (OSX)

@@ -4,6 +4,6 @@
 # This is necessary so that the open file dialog is shown properly
 export MPLBACKEND="TkAgg"
 # Run FlowCal
-python -m FlowCal.excel_ui -v -p
+python -m FlowCal.excel_ui -v -p -H
 # Pause
 read -p "Press [Enter] to finish..."

Run FlowCal (Windows).bat

@@ -1,6 +1,6 @@
 :: Not show commands
 @echo off
 :: Run FlowCal
-python -m FlowCal.excel_ui -v -p
+python -m FlowCal.excel_ui -v -p -H
 :: Pause
 set /p=Press [Enter] to finish...

test/test_gate.py

@@ -892,6 +892,30 @@ def test_gate_fraction_2_mask(self):
                 0,0,0,0,0,0], dtype=bool)
             )
 
+    # Test error when gate_fraction outside [0,1]
+
+    def test_gate_fraction_2_error_negative_gate_fraction(self):
+        bins = [-0.5, 0.5, 1.5, 2.5, 3.5, 4.5]
+        self.assertRaises(
+            ValueError,
+            FlowCal.gate.density2d,
+            self.pyramid,
+            bins=bins,
+            gate_fraction=-0.1,
+            sigma=0.0,
+            )
+
+    def test_gate_fraction_2_error_large_gate_fraction(self):
+        bins = [-0.5, 0.5, 1.5, 2.5, 3.5, 4.5]
+        self.assertRaises(
+            ValueError,
+            FlowCal.gate.density2d,
+            self.pyramid,
+            bins=bins,
+            gate_fraction=1.1,
+            sigma=0.0,
+            )
+
     # Test implicit gating (when values exist outside specified bins)
     #
     # The expected behavior is that density2d() should mimic