Merge pull request #423 from rafalkowalewski1/development

Development

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.5
+current_version = 0.6.6
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.readthedocs.yaml

@@ -26,7 +26,7 @@ sphinx:
 # Optional but recommended, declare the Python requirements required
 # to build your documentation
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: requirements.txt
-#    - method: pip
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip

changelog.rst

@@ -1,7 +1,17 @@
 Changelog
 =========
 
-Last change: 22-OCT-2023 MTS
+Last change: 05-DEC-2023 MTS
+
+0.6.6
+-----
+- 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)
 
 0.6.3 - 0.6.5
 -------------
@@ -14,6 +24,7 @@ Last change: 22-OCT-2023 MTS
 - Fix test clusterer HDBSCAN bug
 - Fix .nd2 localized files info loading (full loader changed to unsafe loader)
 - Fix rare bug with pick similar zero division error
+- Update installation instructions
 
 0.6.2
 -----

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.6.5
+AppVersion=0.6.6
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.6.5"
+OutputBaseFilename="Picasso-Windows-64bit-0.6.6"
 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 = "0.6.5"
+release = "0.6.6"
 
 # -- General configuration ---------------------------------------------------
 

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx==5.3.0
+sphinx_rtd_theme==1.1.1
+readthedocs-sphinx-search==0.1.1

picasso/__init__.py

@@ -3,12 +3,12 @@
     ~~~~~~~~~~~~~~~~~~~~
 
     :authors: Joerg Schnitzbauer, Maximilian Thomas Strauss, Rafal Kowalewski 2016-2023
-    :copyright: Copyright (c) 2016-2018 Jungmann Lab, MPI of Biochemistry
+    :copyright: Copyright (c) 2016-2023 Jungmann Lab, MPI of Biochemistry
 """
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.6.5"
+__version__ = "0.6.6"
 
 _this_file = _ospath.abspath(__file__)
 _this_dir = _ospath.dirname(_this_file)

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.6.5"
+VERSION_NO = "0.6.6"

picasso/clusterer.py

@@ -385,14 +385,15 @@ def dbscan(locs, radius, min_density, pixelsize=None):
     Paramters
     ---------
     locs : np.recarray
-        Localizations to be clustered
+        Localizations to be clustered.
     radius : float
-        DBSCAN search radius, often referred to as "epsilon"
+        DBSCAN search radius, often referred to as "epsilon". Same units
+        as locs.
     min_density : int
         Number of localizations within radius to consider a given point 
-        a core sample
-    pixelsize : int
-        Camera pixel size in nm
+        a core sample.
+    pixelsize : int (default=None)
+        Camera pixel size in nm. Only needed for 3D.
     
     Returns
     -------

picasso/design_sequences.py

@@ -195,5 +195,5 @@
     ["7xR3", "TCCTCTCTCTCTCTCTCTCTC"],
     ["7xR4", "CAACACACACACACACACACA"],
     ["5xR5", "CCCTTCTTCTTCTTCTTCTTC"],
-    ["5xR6", "AAAACAACAACAACAACAACAA"]
+    ["5xR6", "AAAACAACAACAACAACAACAA"],
 ]

picasso/gui/render.py

@@ -5698,7 +5698,9 @@ def add(self, path, render=True):
         self.window.dataset_dialog.add_entry(path)
 
         self.window.setWindowTitle(
-            "Picasso: Render. File: {}".format(os.path.basename(path))
+            "Picasso v{}: Render. File: {}".format(
+                __version__, os.path.basename(path)
+            )
         )
 
         # fast rendering add channel
@@ -7009,7 +7011,7 @@ def save_channel(self, title="Choose a channel"):
             return None
         elif n_channels == 1:
             return 0
-        elif len(self.locs_paths) > 1:
+        elif n_channels > 1:
             pathlist = list(self.locs_paths)
             pathlist.append("Apply to all sequentially")
             pathlist.append("Combine all channels")
@@ -7099,9 +7101,12 @@ def get_render_kwargs(self, viewport=None):
         """
 
         # blur method
-        blur_button = (
-            self.window.display_settings_dlg.blur_buttongroup.checkedButton()
-        )
+        if self._pan: # no blur when panning
+            blur_method = None
+        else: # selected method
+            blur_method = self.window.display_settings_dlg.blur_methods[
+                self.window.display_settings_dlg.blur_buttongroup.checkedButton()
+            ]
 
         # oversampling
         optimal_oversampling = (
@@ -7140,9 +7145,7 @@ def get_render_kwargs(self, viewport=None):
         return {
             "oversampling": oversampling,
             "viewport": viewport,
-            "blur_method": self.window.display_settings_dlg.blur_methods[
-                blur_button
-            ],
+            "blur_method": blur_method,
             "min_blur_width": float(
                 self.window.display_settings_dlg.min_blur_width.value()
             ),
@@ -7411,6 +7414,7 @@ def mouseReleaseEvent(self, event):
                 self._pan = False
                 self.setCursor(QtCore.Qt.ArrowCursor)
                 event.accept()
+                self.update_scene()
             else:
                 event.ignore()
         elif self._mode == "Pick":

picasso/gui/rotation.py

@@ -12,65 +12,26 @@
 
 import os
 import colorsys
-import re
 from functools import partial
 
 import numpy as np
 import matplotlib.pyplot as plt
-from moviepy.video.io.ImageSequenceClip import ImageSequenceClip
+# from moviepy.video.io.ImageSequenceClip import ImageSequenceClip
+import imageio
 from PyQt5 import QtCore, QtGui, QtWidgets
 
 from numpy.lib.recfunctions import stack_arrays
 
 from .. import io, render
-from ..lib import StatusDialog, ProgressDialog
+from ..lib import ProgressDialog
 
-# from icecream import ic #TODO: delete
 
 DEFAULT_OVERSAMPLING = 1.0
 INITIAL_REL_MAXIMUM = 0.5
 N_GROUP_COLORS = 8
 SHIFT = 0.1
 ZOOM = 9 / 7
 
-def atoi(text):
-    """ 
-    Converts string to digit if it represents an integer.
-
-    Parameters
-    ----------
-    text : str
-        String to be converted
-
-    Returns
-    -------
-    int or str
-        int if text represents a digit, text otherwise
-    """
-
-    return int(text) if text.isdigit() else text
-
-def natural_keys(text):
-    """
-    Splits text into three parts:
-        * str ending with "/frame_"
-        * int with frame index
-        * ".png"
-    Using this key, frames' paths can be sorted by their index
-    
-    Parameters
-    ----------
-    text : str
-        String to be split and converted
-
-    Returns
-    -------
-    list
-        Text split into several parts, where strings representing
-        digits are converted to int
-    """
-
-    return [atoi(c) for c in re.split('([0-9]+)', text)]
 
 def get_colors(n_channels):
     """ 
@@ -651,75 +612,31 @@ def build_animation(self):
             if height % 2 == 1:
                 height += 1
 
-            # create temporary folder to store all frames
-            base = os.path.dirname(self.window.view_rot.paths[0])
-            path = os.path.join(base, "animation_frames")
+            # render all frames and save in RAM
+            video_writer = imageio.get_writer(name, fps=self.fps.value())
             progress = ProgressDialog(
                 "Rendering frames", 0, len(angx), self.window
             )
             progress.set_value(0)
-            try:
-                os.mkdir(path)
-                for i in range(len(angx)):
-                    qimage = self.window.view_rot.render_scene(
-                        viewport=[(ymin[i], xmin[i]), (ymax[i], xmax[i])],
-                        ang=(angx[i], angy[i], angz[i]),
-                        animation=True,
-                    )
-                    qimage = qimage.scaled(
-                        width, 
-                        height,
-                        # QtCore.Qt.KeepAspectRatioByExpanding,
-                    )
-                    qimage.save(path + "/frame_{}.png".format(i+1))
-                    progress.set_value(i+1)
-            except:
-                # if folder exists, ask if it should be used or deleted
-                m = QtWidgets.QMessageBox()
-                m.setWindowTitle("Frames already exist")
-                ret = m.question(
-                    self,
-                    "",
-                    "Use the existing frames folder?",
-                    m.Yes | m.No,
+            for i in range(len(angx)):
+                qimage = self.window.view_rot.render_scene(
+                    viewport=[(ymin[i], xmin[i]), (ymax[i], xmax[i])],
+                    ang=(angx[i], angy[i], angz[i]),
+                    animation=True,
                 )
-                if ret == m.No:
-                    # use new frames (render each one) and save
-                    for file in os.listdir(path):
-                        os.remove(os.path.join(path, file))
-                    for i in range(len(angx)):
-                        qimage = self.window.view_rot.render_scene(
-                            viewport=[(ymin[i], xmin[i]), (ymax[i], xmax[i])],
-                            ang=(angx[i], angy[i], angz[i]),
-                            animation=True,
-                        )
-                        qimage = qimage.scaled(
-                            width,
-                            height,
-                            # QtCore.Qt.KeepAspectRatioByExpanding,
-                        )
-                        qimage.save(path + "/frame_{}.png".format(i+1))
-                        progress.set_value(i+1)
-                elif ret == m.Yes:
-                    # use old frames
-                    progress.set_value(len(angx))
-
-            # build a video and save it
-            status = StatusDialog("Creating the video...", self.window)
-            image_files = [
-                os.path.join(path, img)
-                for img in os.listdir(path)
-                if img.endswith(".png")
-            ] # paths to each frame
-            image_files.sort(key=natural_keys) # sort frames
-            video = ImageSequenceClip(image_files, fps=self.fps.value())
-            video.write_videofile(name, logger=None)
-
-            # delete animation frames
-            for file in os.listdir(path):
-                os.remove(os.path.join(path, file))
-            os.rmdir(path)
-            status.close()
+                qimage = qimage.scaled(width, height)
+
+                # convert to a np.array and append
+                ptr = qimage.bits()
+                ptr.setsize(height * width * 4)
+                frame = np.frombuffer(ptr, np.uint8).reshape((width, height, 4))
+                frame = frame[:, :, :3]
+                frame = frame[:, :, ::-1] # invert RGB to BGR
+
+                video_writer.append_data(frame)
+                progress.set_value(i+1)
+            progress.close()
+            video_writer.close()
 
 
 class ViewRotation(QtWidgets.QLabel):
@@ -2287,7 +2204,7 @@ def __init__(self, window):
         rotation_action.triggered.connect(self.view_rot.rotation_input)
         rotation_action.setShortcut("Ctrl+Shift+R")
 
-        delete_rotation_action = view_menu.addAction("Remove rotation")
+        delete_rotation_action = view_menu.addAction("Reset rotation")
         delete_rotation_action.triggered.connect(self.view_rot.delete_rotation)
         delete_rotation_action.setShortcut("Ctrl+Shift+W")
         fit_in_view_action = view_menu.addAction("Fit image to window")

picasso/postprocess.py

@@ -1038,8 +1038,8 @@ def link_loc_groups(locs, info, link_group, remove_ambiguous_lengths=True):
 
 def localization_precision(photons, s, bg, em):
     """
-    Calculates the theoretical localization precision
-    according to Mortensen et al., Nat Meth, 2010
+    Calculates the theoretical localization precision according to
+    Mortensen et al., Nat Meth, 2010 for a 2D unweighted Gaussian fit.
     """
     s2 = s**2
     sa2 = s2 + 1 / 12