def locs_glob_map(func, pattern, args=[], kwargs={}, extension=''):
'''
Maps a function to localization files, specified by a unix style path pattern.
The function must take two arguments: locs and info. It may take additional args and kwargs which
are supplied to this map function.
A new locs file will be saved if an extension is provided. In that case the mapped function must return
new locs and a new info dict.
'''
paths = _glob.glob(pattern)
for path in paths:
locs, info = _io.load_locs(path)
result = func(locs, info, path, *args, **kwargs)
if extension:
base, ext = _ospath.splitext(path)
out_path = base + '_' + extension + '.hdf5'
locs, info = result
_io.save_locs(out_path, locs, info)
def load_locs(path):
"""
Returns localization .hdf5 from picasso as pandas.DataFrame and corresponding .yaml as list of dictionaries.
Args:
path (str): Path to .hdf5 file as generated by `picasso.localize`_
container (str):
Name of dataset within .hdf5 container. Must be set to:
* ``'locs'`` for _locs, _render and _picked .hdf5 files as generated by `picasso.render`_.
* ``'groups'`` for _pickprops.hdf5 files as generated by `picasso.render`_.
* Defaults to ``'locs'``.
Returns:
tuple:
- [0] (pandas.DataFrame): Localizations stored under ``'locs'`` in .hdf5 file
- [1] (list): List of dictionaries contained in .yaml corresponding to .hdf5 file
"""
locs, info = io.load_locs(path)
locs = pd.DataFrame(locs)
return locs, info
############################################ Set parameters
params = {}
# params ={'mng':250}
#%%
############################################ Main loop
paths=[os.path.join(dir_names[i],file_name) for i, file_name in enumerate(file_names)]
failed_path=[]
for path in paths:
### Try loading movie or localizations
try:
try:
file,info=io.load_movie(path) # Load movie
except:
file,info=io.load_locs(path) # Load _locs
out=localize.main(file,info,path,**params)
except Exception:
traceback.print_exc()
failed_path.extend([path])
print()
print('Failed attempts: %i'%(len(failed_path)))
#%%
file_names = []
file_names.extend(
['id200_5000pM_p40uW_exp400_1_MMStack_Pos0.ome_locs_render.hdf5'])
############################################ Set parameters
params = {'pick_diameter': 10, 'min_n_locs': 5000}
#%%
failed_path = []
for i in range(0, len(file_names)):
### Create path
path = os.path.join(dir_names[i], file_names[i])
### Run main function
try:
locs, info = io.load_locs(path)
out = autopick.main(locs, info, path, **params)
except Exception:
traceback.print_exc()
failed_path.extend([path])
print()
print('Failed attempts: %i' % (len(failed_path)))
#%%
############################################ Checkout single files
# i=0
# params={'oversampling':5,
# 'pick_box':11, # Usually 2*oversampling+1
# 'min_n_locs':225,
file_names = []
file_names.extend([
'04_FOV1_Cy3B_p038uW_R1s1-8-100pM_POC_1_MMStack_Pos0.ome_locs_render.hdf5'
])
file_names.extend([
'09_FOV1_Cy3B_p038uW_R1s1-8-050pM_POC_1_MMStack_Pos0.ome_locs_render.hdf5'
])
### Create paths
path = [
os.path.join(dir_names[i], file_names[i]) for i in range(len(file_names))
]
### Load data
locs_ref, info_ref = io.load_locs(path[0])
locs, info = io.load_locs(path[1])
#%%
############################################# Shift
### Define shift
dx = 21
dy = -4
oversampling = 1
c_min = 0
c_max = 500
x_center = 300
x_width = 100
y_center = 300
y_width = 100
import picasso.io as io
import picasso.render as render
import picasso_addon.autopick as autopick
############################################# Load raw data
dir_names = []
dir_names.extend([
r'C:\Data\p17.lbFCS2\21-04-21_EGFR_2xCTC\09_w5-250pM_Cy3B-CTween-c2500_561-p50uW-s75_Pos0-4_1\pick_test'
])
file_names = []
file_names.extend(['render_picked_render.hdf5'])
path = os.path.join(dir_names[0], file_names[0])
locs_in, info = io.load_locs(path)
############################################# Render
oversampling = 5
image = render.render(
locs_in,
info,
oversampling=oversampling,
)[1]
############################################# Identify pick centers
pick_box = 11
min_n_locs = 120
centers_image, fit = autopick.spotcenters_in_image(image,
pick_box,
min_n_locs,
r'C:\Users\flori\Documents\mpi\repos\lbFCS\styles\paper.mplstyle')
############################################# Define data
dir_names = []
dir_names.extend([
r'C:\Data\p06.SP-tracking\20-01-16_immob-th_pseries_livecell\id169_R1-54#_R1s1-8_40nM_exp200_p114uW_T21_1'
])
file_names = []
file_names.extend([
'id169_R1-54#_R1s1-8_40nM_exp200_p114uW_T21_1_MMStack_Pos0.ome_locs_render_picked_query_avg3_render.hdf5'
])
############################################ Load data
path = [os.path.join(dir_names[i], f)
for i, f in enumerate(file_names)] # Path
locs, info = io.load_locs(path[0]) # Load _locs
#%%
################ Get rendered image
xy_lim = [349.7, 350.3]
oversampling = 40
image = render.render(
locs,
info=None,
oversampling=oversampling,
viewport=[(xy_lim[0], xy_lim[0]), (xy_lim[1], xy_lim[1])],
blur_method=None,
min_blur_width=0,
)[1]
################ Lineplot histogram through center and fitting
### Get line