SCGV viewer supports batch mode...

KrasnitzLab · Apr 16, 2019 · 22ac95a · 22ac95a
1 parent ce78bbe
commit 22ac95a
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Showing 4 changed files with 50 additions and 5 deletions.
diff --git a/scgv/qtmain.py b/scgv/qtmain.py
@@ -8,6 +8,8 @@
 from PyQt5.QtWidgets import QApplication
 
 from scgv.qtviews.main_window import MainWindow
+from scgv.models.model import DataModel
+from scgv.qtviews.canvas import Canvas
 
 import os
 import traceback
@@ -53,12 +55,57 @@ def main(argv=None):
             '-V', '--version',
             action='version', version=program_version_message)
 
+        parser.add_argument(
+            '-d', '--directory',
+            type=str,
+            dest='directory',
+            metavar='<dir name>',
+            help='load data from directory')
+
+        parser.add_argument(
+            '-o', '--output',
+            type=str,
+            dest='output',
+            metavar='<output filename>',
+            help='saves main view in a figure with specified filename')
+
+        parser.add_argument(
+            '-t', '--title',
+            type=str,
+            dest='title',
+            metavar='<figure title>',
+            help='adds title to the saved figure')
+
+        parser.add_argument(
+            '-r', '--resolution',
+            type=int,
+            dest='resolution',
+            metavar='<resolution>',
+            help='figure output resolution',
+            default=300)
+
         args = parser.parse_args()
         print(args)
 
+        if args.directory is not None and args.output is not None:
+            assert os.path.exists(args.directory)
+            model = DataModel(args.directory)
+            model.make()
+
+            canvas = Canvas()
+            canvas.model = model
+            canvas.redraw()
+            if args.title is not None:
+                canvas.fig.suptitle(args.title, fontsize=24)
+
+            canvas.fig.savefig(args.output, dpi=args.resolution)
+            return 0
+
         app = QApplication(sys.argv)
         window = MainWindow()
         window.show()
+        if args.directory is not None:
+            window.open_buttons.load_model(args.directory)
         app.exec_()
 
         return 0

diff --git a/scgv/qtviews/canvas.py b/scgv/qtviews/canvas.py
@@ -40,7 +40,7 @@ class Canvas(FigureCanvas):
 
     def __init__(self, has_dendro=True):
         self.model = None
-        self.fig = Figure(figsize=(12, 8))
+        self.fig = Figure(figsize=(24, 16))
         super(Canvas, self).__init__(self.fig)
         self.has_dendro = has_dendro
         self.signals = CanvasSignals()

diff --git a/scgv/qtviews/main_window.py b/scgv/qtviews/main_window.py
@@ -98,7 +98,7 @@ def __init__(self, window):
     def on_open_directory_click(self, s):
         dirname = QFileDialog.getExistingDirectory(
             self.window, "Open Directory")
-        self._load_model(dirname)
+        self.load_model(dirname)
 
     def on_open_archive_click(self, s):
         filter = "Zip File (*.zip)"
@@ -107,7 +107,7 @@ def on_open_archive_click(self, s):
             ".", filter)
         self._load_model(filename)
 
-    def _load_model(self, filename):
+    def load_model(self, filename):
 
         self.open_archive_action.setEnabled(False)
         self.open_dir_action.setEnabled(False)

diff --git a/scgv/views/clone.py b/scgv/views/clone.py
@@ -34,7 +34,6 @@ def _select_colormap(self):
         self.cmap = self._select_colormap_size(size)
 
     def draw_clone(self, ax):
-        print(self.model.clone)
 
         if self.model.clone is not None:
             ax.imshow(
@@ -53,7 +52,6 @@ def draw_clone(self, ax):
         ax.set_yticklabels(["Clone"])
 
     def draw_subclone(self, ax):
-        print(self.model.subclone)
         if self.model.subclone is not None:
             ax.imshow(
                 [self.model.subclone],