Merge pull request #432 from rafalkowalewski1/development

Development

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.7
+current_version = 0.6.8
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.10
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v2
       with:
         python-version: 3.10.13
     - name: Install dependencies

changelog.rst

@@ -1,17 +1,20 @@
 Changelog
 =========
 
-Last change: 10-JAN-2024 MTS
+Last change: 23-JAN-2024 MTS
 
-0.6.6 - 0.6.7
+0.6.6 - 0.6.8
 -------------
 - GUI modules display the Picasso version number in the title bar
 - Added readthedocs requirements file (only for developers)
 - No blur applied when padding in Picasso: Render (increases speed of rendering)
 - Camera settings saved in the .yaml file after localization
 - Picasso: Design has the speed optimized extension sequences (Strauss and Jungmann, Nature Methods, 2020)
 - Change matplotlib backend for macOS (bug fix with some plots being unavailable)
-- Build animation does not trigger antivirus, which could delete Picasso (one click installer only)
+- .tiff files can be loaded to Localize directly, *although the support may limited!*
+- Bug fix: build animation does not trigger antivirus, which could delete Picasso (one click installer only)
+- Bug fix: 2D cluster centers area and convex hull are saved correctly
+- Bug fix: rectangular picks
 
 0.6.3 - 0.6.5
 -------------

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.6.7
+AppVersion=0.6.8
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.7"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.8"
 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 = "0.6.7"
+release = "0.6.8"
 
 # -- General configuration ---------------------------------------------------
 

picasso/__init__.py

@@ -8,7 +8,7 @@
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.6.7"
+__version__ = "0.6.8"
 
 _this_file = _ospath.abspath(__file__)
 _this_dir = _ospath.dirname(_this_file)

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.6.7"
+VERSION_NO = "0.6.8"

picasso/clusterer.py

@@ -618,8 +618,8 @@ def find_cluster_centers(locs, pixelsize=None):
             dtype=CLUSTER_CENTERS_DTYPE_3D,
         )
     else:
-        area = _np.array([_[13] for _ in centers_])
-        convexhull = _np.array([_[14] for _ in centers_])
+        area = _np.array([_[15] for _ in centers_])
+        convexhull = _np.array([_[16] for _ in centers_])
         centers = _np.rec.array(
             (
                 frame,

picasso/gui/localize.py

@@ -144,7 +144,7 @@ def drop_has_valid_url(self, event):
             return False
         path, extension = self.path_from_drop(event)
 
-        if extension.lower() not in [".raw", ".tif", ".ims", ".nd2"]:
+        if extension.lower() not in [".raw", ".tif", ".ims", ".nd2", ".tiff"]:
             return False
         return True
 
@@ -1237,11 +1237,12 @@ def open_file_dialog(self):
             "Open image sequence", 
             directory=dir, 
             filter=(
-                "All supported formats (*.raw *.tif *.tif *.nd2 *.ims)"
+                "All supported formats (*.raw *.tif *.nd2 *.ims *.tiff)"
                 ";;Raw files (*.raw)"
                 ";;Tif images (*.tif)"
                 ";;ImaRIS IMS (*.ims)"
                 ";;Nd2 files (*.nd2);;"
+                ";;Tiff images (*.tiff)"
             )
         )
         if path:

picasso/gui/render.py

@@ -3315,7 +3315,7 @@ def calculate_nena_lp(self):
             progress = lib.ProgressDialog(
                 "Calculating NeNA precision", 0, 100, self
             )
-            result_lp = postprocess.nena(locs, info, progress.set_value)
+            result_lp = postprocess.nena(locs.copy(), info, progress.set_value)
 
             # modify the movie grid
             if not self.nena_calculated: # if nena calculated first time
@@ -6055,7 +6055,7 @@ def _dbscan(self, channel, path, params):
         if save_centers:
             status = lib.StatusDialog("Calculating cluster centers", self)
             path = path.replace(".hdf5", "_cluster_centers.hdf5")
-            centers = clusterer.find_cluster_centers(locs, pixelsize=pixelsize)
+            centers = clusterer.find_cluster_centers(locs, pixelsize=pixelsize)     
             io.save_locs(path, centers, self.infos[channel] + [dbscan_info])
             status.close()
 
@@ -6417,14 +6417,14 @@ def get_pick_rectangle_corners(
             alpha = np.arctan((end_y - start_y) / (end_x - start_x))
         dx = width * np.sin(alpha) / 2
         dy = width * np.cos(alpha) / 2
-        x1 = int(start_x - dx)
-        x2 = int(start_x + dx)
-        x4 = int(end_x - dx)
-        x3 = int(end_x + dx)
-        y1 = int(start_y + dy)
-        y2 = int(start_y - dy)
-        y4 = int(end_y + dy)
-        y3 = int(end_y - dy)
+        x1 = float(start_x - dx)
+        x2 = float(start_x + dx)
+        x4 = float(end_x - dx)
+        x3 = float(end_x + dx)
+        y1 = float(start_y + dy)
+        y2 = float(start_y - dy)
+        y4 = float(end_y + dy)
+        y3 = float(end_y - dy)
         return [x1, x2, x3, x4], [y1, y2, y3, y4]
 
     def get_pick_rectangle_polygon(

picasso/io.py

@@ -184,7 +184,7 @@ def load_movie(path, prompt_info=None, progress=None):
     ext = ext.lower()
     if ext == ".raw":
         return load_raw(path, prompt_info=prompt_info)
-    elif ext == ".tif":
+    elif ext == ".tif" or ext == ".tiff":
         return load_tif(path)
     elif ext == ".ims":
         return load_ims(path, prompt_info=prompt_info)

release/one_click_windows_gui/create_installer_windows.bat

@@ -11,7 +11,7 @@ call conda activate picasso_installer
 call python setup.py sdist bdist_wheel
 
 call cd release/one_click_windows_gui
-call pip install "../../dist/picassosr-0.6.7-py3-none-any.whl"
+call pip install "../../dist/picassosr-0.6.8-py3-none-any.whl"
 
 call pip install pyinstaller==5.7
 call pyinstaller ../pyinstaller/picasso.spec -y --clean

release/one_click_windows_gui/picasso_innoinstaller.iss

@@ -1,10 +1,10 @@
 [Setup]
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
-AppVersion=0.6.7
+AppVersion=0.6.8
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.7"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.8"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="picassosr",
-    version="0.6.7",
+    version="0.6.8",
     author="Joerg Schnitzbauer, Maximilian T. Strauss, Rafal Kowalewski",
     author_email=("joschnitzbauer@gmail.com, straussmaximilian@gmail.com, rafalkowalewski998@gmail.com"),
     url="https://github.com/jungmannlab/picasso",