Modif GUI

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.3
+current_version = 0.7.5
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

changelog.rst

@@ -1,13 +1,32 @@
 Changelog
 =========
 
-Last change: 02-OCT-2024 MTS
+Last change: 06-FEB-2025 MTS
 
-0.7.1 - 0.7.3
+0.7.5
+-----
+- Automatic picking of fiducials added in Render: ``Tools/Pick fiducials``
+- Undrifting from picked moved from ``picasso/gui/render`` to ``picasso/postprocess``
+- Plugin docs update
+- Filter histogram display fixed for datasets with low variance (bug fix)
+- AIM undrifting works now if the first frames of localizations are filtered out (bug fix)
+- 2D drift plot in Render inverts y axis to match the rendered localizations
+- 3D animation fixed
+- Other minor bug fixes
+
+0.7.1 - 0.7.4
 -------------
 - SMLM clusterer in picked regions deleted
 - Show legend in Render property displayed rounded tick label values
 - Pick circular area does not save the area for each pick in localization's metadata 
+- Picasso: Render - adjust the scale bar's size automatically based on the current FOV's width
+- Picasso: Render - RESI dialog fixed, units in nm
+- Picasso: Render - show drift in nm, not camera pixels
+- Picasso: Render - masking localizations saves the mask area in its metadata
+- Picasso: Render - export current view across channels in grayscale
+- Picasso: Render - title bar displays the file only the names of the currently opened files
+- CMD implementation of AIM undrifting, see ``picasso aim -h`` in terminal
+- CMD localize saves camera information in the metadata file
 - Other minor bug fixes
 
 0.7.0

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.7.3
+AppVersion=0.7.5
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.7.3"
+OutputBaseFilename="Picasso-Windows-64bit-0.7.5"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/cmd.rst

@@ -78,6 +78,10 @@ undrift
 -------
 Correct localization coordinates for drift with RCC.
 
+aim
+-------
+Correct localization coordinates for drift with AIM.
+
 density
 -------
 Compute the local density of localizations

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.7.3"
+release = "0.7.5"
 
 # -- General configuration ---------------------------------------------------
 

docs/plugins.rst

@@ -4,34 +4,33 @@ Plugins
 
 Usage
 -----
-Starting in version 0.5.0, Picasso allows for creating plugins. They can be added by the user for each of the available distributions of picasso (GitHub, picassosr from PyPI and the one click installer). However, using plugins in the latter may cause issues, see below.
+Starting in version 0.5.0, Picasso supports plugins. Please find the instructions on how to add them to your Picasso below. 
 
-Please keep in mind that the ``__init__.py`` file in the ``plugins`` folder must not be modified or deleted.
+Please keep in mind that the ``__init__.py`` file in the ``picasso/picasso/gui/plugins`` folder must not be modified or deleted.
 
 GitHub
 ~~~~~~
+If you cloned the GitHub repository, you can add plugins by following these steps:
 - Find the directory where you cloned the GitHub repository with Picasso.
 - Go to ``picasso/picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
-- The plugin(s) should automatically work after running picasso in the new command window.
 
 PyPI
 ~~~~
-- Find the location of the environment where picassosr is installed (type ``conda env list`` to see the directory).
-- Find this directory and go to ``YOUR_ENVIRONMENT/Lib/site-packages/picasso/gui/plugins``.
+If you installed Picasso using ``pip install picassosr``, you can add plugins by following these steps:
+- To find the location of the environment where ``picassosr`` is installed, type ``conda env list``.
+- If your environment can be found under ``YOUR_ENVIRONMENT``, go to ``YOUR_ENVIRONMENT/Lib/site-packages/picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
-- The plugin(s) should automatically work after running picasso in the new command window.
 
 One click installer
 ~~~~~~~~~~~~~~~~~~~
-**NOTE**: This may lead to issues if Picasso is installed, as the plugin scripts will remain in the ``plugins`` folder upon deinstallation. After deinstalltion, the ``Picasso`` folder needs to be deleted manually.
+**NOTE**: After deinstalling Picasso, ``Program Files/Picasso`` folder needs to be deleted manually, as the uninstaller currently does not remove the plugins automatically.
 
 - Find the location where you installed Picasso. By default, it is ``C:/Program Files/Picasso``.
 - Go to the following subfolder in the `Picasso` directory: ``picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
-- The plugin(s) should automatically be loaded after double-clicking the respective desktop shortcuts.
 
-**NOTE**: Plugins added in this distribution will not be able to use packages that are not installed automatically (from the file ``requirements.txt``).
+.. **NOTE**: Plugins added in this distribution will not be able to use packages that are not installed automatically (from the file ``requirements.txt``).
 
 For developers
 --------------
@@ -41,4 +40,4 @@ To create a plugin, you can use the template provided in ``picasso/plugin_templa
    :scale: 70 %
    :alt: Plugins
 
-As an example, please see any of the plugins on the GitHub `repo <https://github.com/rafalkowalewski1/picasso_plugins>`_.
+As an example, please see any of the plugins in the `GitHub repo <https://github.com/rafalkowalewski1/picasso_plugins>`_.

docs/render.rst

@@ -61,6 +61,8 @@ The 3D rotation window allows the user to render 3D localization data. To use it
 
 The user may perform multiple actions in the rotation window, including: saving rotated localizations, building animations (.mp4 format), rotating by a specified angle, etc.
 
+Note that to build animations, the user must have ``ffmpeg`` installed on their system. 
+
 Rotation around z-axis is available by pressing Ctrl/Command. Rotation axis can be frozen by pressing x/y/z to freeze around the corresponding axes (to freeze around the z-axis, Ctrl/Command must be pressed as well).
 
 There are several things to keep in mind when using the rotation window. Firstly, using individual localization precision is very slow and is not recommended as a default blur method. Also, the size of the rotation window can be altered, however, if it becomes too large, rendering may start to lag.

picasso/__init__.py

@@ -8,7 +8,7 @@
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.7.3"
+__version__ = "0.7.5"
 
 _this_file = _ospath.abspath(__file__)
 _this_dir = _ospath.dirname(_this_file)

picasso/__main__.py

@@ -423,6 +423,26 @@ def _undrift(files, segmentation, display=True, fromfile=None):
         savetxt(base + "_drift.txt", drift, header="dx\tdy", newline="\r\n")
 
 
+def _undrift_aim(
+    files, segmentation, intersectdist=20/130, roiradius=60/130
+):
+    import glob
+    from . import io, aim
+    from numpy import savetxt
+
+    paths = glob.glob(files)
+    for path in paths:
+        try:
+            locs, info = io.load_locs(path)
+        except io.NoMetadataFileError:
+            continue
+        print("Undrifting file {}".format(path))
+        locs, new_info, drift = aim.aim(locs, info, segmentation, intersectdist, roiradius)
+        base, ext = os.path.splitext(path)
+        io.save_locs(base + "_aim.hdf5", locs, new_info)
+        savetxt(base + "_aimdrift.txt", drift, header="dx\tdy", newline="\r\n")  
+
+
 def _density(files, radius):
     import glob
 
@@ -772,7 +792,7 @@ def _localize(args):
     print("Localize - Parameters:")
     print("{:<8} {:<15} {:<10}".format("No", "Label", "Value"))
 
-    if args.fit_method == "lq-gpu":
+    if args.fit_method == "lq-gpu" or args.fit_method == "lq-gpu-3d":
         if gausslq.gpufit_installed:
             print("GPUfit installed")
         else:
@@ -985,6 +1005,7 @@ def prompt_info():
                 print("------------------------------------------")
 
             info.append(localize_info)
+            info.append(camera_info)
 
             base, ext = splitext(path)
 
@@ -1004,7 +1025,7 @@ def prompt_info():
 
             if CHECK_DB:
                 print("\n")
-                print("Assesing quality and adding to DB")
+                print("Assessing quality and adding to DB")
                 add_file_to_db(path, out_path)
                 print("Done.")
                 print("\n")
@@ -1210,12 +1231,12 @@ def main():
             " specified by a unix style path pattern"
         ),
     )
-    undrift_parser.add_argument(
-        "-m",
-        "--mode",
-        default="render",
-        help='"std", "render" or "framepair")',
-    )
+    # undrift_parser.add_argument(
+    #     "-m",
+    #     "--mode",
+    #     default="render",
+    #     help='"std", "render" or "framepair")',
+    # )
     undrift_parser.add_argument(
         "-s",
         "--segmentation",
@@ -1239,6 +1260,48 @@ def main():
         help="do not display estimated drift",
     )
 
+    # undrift by AIM parser
+    undrift_aim_parser = subparsers.add_parser(
+        "aim", help="correct localization coordinates for drift with AIM"
+    )
+    undrift_aim_parser.add_argument(
+        "files",
+        help=(
+            "one or multiple hdf5 localization files"
+            " specified by a unix style path pattern"
+        ),
+    )
+    undrift_aim_parser.add_argument(
+        "-s",
+        "--segmentation",
+        type=float,
+        default=100,
+        help=(
+            "the number of frames to be combined"
+            " for one temporal segment (default=100)"
+        ),
+    )
+    undrift_aim_parser.add_argument(
+        "-i",
+        "--intersectdist",
+        type=float,
+        default=20/130,
+        help=(
+            "max. distance (cam. pixels) between localizations in"
+            " consecutive segments to be considered as intersecting"
+        ),
+    )
+    undrift_aim_parser.add_argument(
+        "-r",
+        "--roiradius",
+        type=float,
+        default=60/130,
+        help=(
+            "max. drift (cam. pixels) between two consecutive"
+            " segments"
+        ),
+    )
+
     # local densitydd
     density_parser = subparsers.add_parser(
         "density", help="compute the local density of localizations"
@@ -1708,6 +1771,8 @@ def main():
             )
         elif args.command == "undrift":
             _undrift(args.files, args.segmentation, args.nodisplay, args.fromfile)
+        elif args.command == "aim":
+            _undrift_aim(args.files, args.segmentation, args.intersectdist, args.roiradius)
         elif args.command == "density":
             _density(args.files, args.radius)
         elif args.command == "dbscan":

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.7.3"
+VERSION_NO = "0.7.5"

picasso/aim.py

@@ -628,12 +628,15 @@ def aim(
         Radius of the local search region in camera pixels. Should be 
         larger than the  maximum expected drift within segmentation.
     progress : picasso.lib.ProgressDialog (default=None)
-        Progress dialog. If None, progress is displayed with tqdm.
+        Progress dialog. If None, progress is displayed with into the 
+        console.
 
     Returns
     -------
     locs : _np.rec.array
         Undrifted localizations.
+    new_info : list of 1 dict
+        Updated metadata.
     drift : _np.rec.array
         Drift in x and y directions (and z if applicable).
     """
@@ -649,14 +652,18 @@ def aim(
         if val := inf.get("Height"):
             height = val
         if val := inf.get('Frames'):
-            n_frames = val
+            n_frames = val - locs["frame"].min()
         if val := inf.get("Pixelsize"):
             pixelsize = val
     if _np.isnan(width * height * pixelsize * n_frames):
-        raise KeyError("Insufficient metadata available.")
+        raise KeyError(
+            "Insufficient metadata available. Please specify 'Width', 'Height',"
+            " 'Frames' and 'Pixelsize' in the metadata .yaml."
+        )
 
     # frames should start at 1 
-    frame = locs["frame"] + 1
+    frame = locs["frame"] + 1 - locs["frame"].min()
+
     # find the segmentation bounds (temporal intervals)
     seg_bounds = _np.concatenate((
         _np.arange(0, n_frames, segmentation), [n_frames]
@@ -686,9 +693,13 @@ def aim(
     drift_x = drift_x1 + drift_x2
     drift_y = drift_y1 + drift_y2
 
-    # # shift the drifts by the mean value
-    drift_x -= _np.mean(drift_x)
-    drift_y -= _np.mean(drift_y)
+    # shift the drifts by the mean value
+    shift_x = _np.mean(drift_x)
+    shift_y = _np.mean(drift_y)
+    drift_x -= shift_x
+    drift_y -= shift_y
+    x_pdc += shift_x
+    y_pdc += shift_y
 
     # combine to Picasso format
     drift = _np.rec.array((drift_x, drift_y), dtype=[("x", "f"), ("y", "f")])
@@ -713,7 +724,9 @@ def aim(
             aim_round=2, progress=progress,
         )
         drift_z = drift_z1 + drift_z2
-        drift_z -= _np.mean(drift_z)
+        shift_z = _np.mean(drift_z)
+        drift_z -= shift_z
+        z_pdc += shift_z
         drift = _np.rec.array(
             (drift_x, drift_y, drift_z), 
             dtype=[("x", "f"), ("y", "f"), ("z", "f")]
@@ -726,7 +739,7 @@ def aim(
         locs["z"] = z_pdc
 
     new_info = {
-        "Undrifted by": "AIM",
+        "Generated by": "AIM undrift",
         "Intersect distance (nm)": intersect_d * pixelsize,
         "Segmentation": segmentation,
         "Search regions radius (nm)": roi_r * pixelsize,

picasso/gausslq.py

@@ -14,7 +14,7 @@
 from tqdm import tqdm as _tqdm
 import numba as _numba
 import multiprocessing as _multiprocessing
-from concurrent import futures as _futures
+from concurrent         import futures as _futures
 from . import postprocess as _postprocess
 
 try:
@@ -81,7 +81,6 @@ def _initial_parameters(spot, size, size_half):
 
 
 def initial_parameters_gpufit(spots, size):
-
     center = (size / 2.0) - 0.5
     initial_width = _np.amax([size / 5.0, 1.0])
 
@@ -155,7 +154,7 @@ def fit_spot(spot):
 
 def fit_spots(spots):
     theta = _np.empty((len(spots), 6), dtype=_np.float32)
-    theta.fill(_np.nan)
+    # theta.fill(_np.nan)
     for i, spot in enumerate(spots):
         theta[i] = fit_spot(spot)
     return theta