rgerum / saenopy Goto Github PK

Copy progress bar or latest command lines in viewer, to also see in the viewer that there is some progress

On mobile devices or small windows the menu menu/hamburger is not clickable. Also the footer "v:latest" is not expandable.
This seems to be related to the "sphinx_rtd_theme":
readthedocs/readthedocs.org#4132
readthedocs/readthedocs.org#3925

However, when I build Readthedocs locally (with same versions of sphinx_rtd_theme), I do not encounter this problem.

Could it be related to the optional keyword here ?
sphinx-rtd-theme = { version = "^1.1.1", optional = true }
nbsphinx = { version = "^0.8.10", optional = true }
sphinx-gallery = {version = "^0.11.1", optional = true }

I think this produces wrong values for "start" and "end", resulting in only one z-slice being displayed, no matter which z_range:
z_range = [0, 5, 10, 1000][params["stack"]["z_proj"]]
start = np.clip(params["stack"]["z"] - z_range, 0, stack.shape[2])
end = np.clip(params["stack"]["z"] + z_range, 0, stack.shape[2])

Setting im = stack[:, :, :, 0:11] manually fixed the problem for my stack.

Add comment (or function) that explains how read in Solver objects instead of the get_stack function, in case the user wants to run only parts of the script again

ToDo: Think of adding filtered cell image below the 3D plot for better orientation (optional: dialog to read in any image)

Add colorbar also to the pyTFM user interface for deformations and tractions (so far only in the saved plots).

Make colorbar in the ExportImage Dialog optional.

May add a option for reversing ("_r") each colormaps in the selection dialog.

Think of an option / parameter to select the mode for calculating the cell center to be used for the total contractility, either based on deformation field (probably the interpolated field) or on the force field.

Then also for time lines, if a single center from a time step (first/last) should be used for all time steps (e.g. could be used for stationary spheroids) or continuously centers (default).

• Reference stack: Either Single Timpoint or "Accumulating" between timesteps
• Active: Single timepoint or timeseries

Check if channel number is the same in both cases

Add full maximumprojection option and think about using single button instead of several buttons. Also think of µm or z-slices

Bounding box sizes increases/decreases size dependend on Piv arrow size

• Option for Erasing Drawn cell masks (or explain that ALT shortkey allows this)
• Use contractility or strain energy as default parameter in the Evaluation menu, so that "normal" TFM with single cells does not start with a missing error dialog, since no stresses between cells can be calculated

Progress bar is sofar showing progress for each solver object, and starts over for each timestep. Would be nice to see the current timestep also (maybe overlaid or below). E.g. "Current Filename" t=2/20

Add Example for "Data Analysis"

Analysis for single object seems to work. However, when reading in mutiple cells simultaniously, the alive / relaxed images are not
displayed correctly (Deformation direction and Analysis seems to be allright, only a visualization problem) and its not possible to change the windowsize for list elements except the first. There seems to be an error in handling mutiple task paralell. Console prints "Cannot queue arguments of type Qvector

Also the read-in Dialog only supports TIF files currently.

• Do not show Aggregate field for single timepoints
• Rename Option with right Click

Cmap option and maybe custom scaling (slider?) for the Arrows

Change how the Alpha parameter is set in the GUI. Maybe we use a 10** [ Input ] or 1e [Input] field in the Viewer.

Create Videos of 3D-Fields and projections for timelines. Also for the 3D rendering, as soon as we have this. In case of only 2 timepoints Gifs with the reference state could be an option.

The saenopy/gui folder is missing an __init__.py file, so the folder is not packaged into the wheel-file and is missing after installing saenopy via pip.