Merge pull request #509 from jungmannlab/development

0.7.4

Author: rafalkowalewski1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.3
+current_version = 0.7.4
 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 +1,21 @@
 Changelog
 =========
 
-Last change: 02-OCT-2024 MTS
+Last change: 14-DEC-2024 MTS
 
-0.7.1 - 0.7.3
+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=0.7.4
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.7.3"
+OutputBaseFilename="Picasso-Windows-64bit-0.7.4"
 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 = "0.7.4"
 
 # -- General configuration ---------------------------------------------------
 

picasso/__init__.py

@@ -8,7 +8,7 @@
 import os.path as _ospath
 import yaml as _yaml
 
-__version__ = "0.7.3"
+__version__ = "0.7.4"
 
 _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
 
@@ -985,6 +1005,7 @@ def prompt_info():
                 print("------------------------------------------")
 
             info.append(localize_info)
+            info.append(camera_info)
 
             base, ext = splitext(path)
 
@@ -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 = "0.7.4"

picasso/aim.py

@@ -634,6 +634,8 @@ def aim(
     -------
     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).
     """
@@ -686,9 +688,13 @@ 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 +719,9 @@ 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 +734,7 @@ 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,