Merge pull request #453 from jungmannlab/development

v0.6.10

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.9
+current_version = 0.6.10
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.readthedocs.yaml

@@ -8,7 +8,11 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python:
+      version: 3.10
+      install:
+        - method: pip
+        - path: .
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

changelog.rst

@@ -1,12 +1,19 @@
 Changelog
 =========
 
-Last change: 22-FEB-2024 MTS
+Last change: 06-JUN-2024 MTS
 
-0.6.9
------
+0.6.9 - 0.6.10
+--------------
 - Added the option to draw polygon picks in Picasso: Render
 - Save pick properties in Picasso: Render saves areas of picked regions in nm^2
+- Calibration .yaml file saves number of frames and step size in nm
+- ``picasso.lib.merge_locs`` function can merge localizations from multiple files
+- Mask dialog in Picasso: Render saves .png mask files
+- Mask dialog in Picasso: Render allows to save .png with the blurred image
+- Picasso: Localize - added the option to save the current view as a .png file
+- Picasso: Render - functions related to picking moved to ``picasso.lib`` and ``picasso.postprocess``
+- Picasso: Render - saving picked localizations saves the area(s) of the picked region(s) in the metadata file (.yaml)
 
 0.6.6 - 0.6.8
 -------------

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.6.9
+AppVersion=0.6.10
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.9"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.10"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.6.9"
+release = "0.6.10"
 
 # -- General configuration ---------------------------------------------------
 

picasso/__init__.py

@@ -8,7 +8,7 @@
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.6.9"
+__version__ = "0.6.10"
 
 _this_file = _ospath.abspath(__file__)
 _this_dir = _ospath.dirname(_this_file)

picasso/__main__.py

@@ -165,15 +165,17 @@ def _hdf2csv(path):
         paths = glob(path)
     if paths:
         import os.path
+        from .io import load_locs
 
         for path in _tqdm(paths):
             base, ext = os.path.splitext(path)
             if ext == ".hdf5":
                 print("Converting {}".format(path))
                 out_path = base + ".csv"
-                locs = pd.read_hdf(path)
+                locs = load_locs(path)[0]
+                df = pd.DataFrame(locs)
                 print("A total of {} rows loaded".format(len(locs)))
-                locs.to_csv(out_path, sep=",", encoding="utf-8")
+                df.to_csv(out_path, sep=",", encoding="utf-8")
     print("Complete.")
 
 

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.6.9"
+VERSION_NO = "0.6.10"

picasso/gui/localize.py

@@ -1145,6 +1145,10 @@ def init_menu_bar(self):
         # save_parameters_action.setShortcut('Ctrl+Shift+S')
         # save_parameters_action.triggered.connect(self.save_parameters)
         # file_menu.addAction(save_parameters_action)
+        file_menu.addSeparator()
+        export_current_action = file_menu.addAction("Export current view")
+        export_current_action.setShortcut("Ctrl+E")
+        export_current_action.triggered.connect(self.export_current)
 
         """ View """
         view_menu = menu_bar.addMenu("View")
@@ -1788,6 +1792,26 @@ def save_spots_dialog(self):
             if path:
                 self.save_spots(path)
 
+    def export_current(self):
+        """ Exports current view as .png or .tif. """
+
+        try:
+            base, ext = os.path.splitext(self.movie_path)
+        except AttributeError:
+            return
+        out_path = base + "_view.png"
+        path, ext = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save image", out_path, filter="*.png;;*.tif"
+        )
+        if path:
+            qimage = QtGui.QImage(self.view.size(), QtGui.QImage.Format_RGB32)
+            painter = QtGui.QPainter(qimage)
+            self.view.render(painter)
+            painter.end()
+            qimage.save(path)
+            # self.view.scene().save_image(path)
+        self.view.setMinimumSize(1, 1)
+
     def save_locs(self, path):
         localize_info = self.last_identification_info.copy()
         localize_info["Generated by"] = "Picasso Localize"