SwissFEL/grum
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

changes at beamline

Browse Source
This commit is contained in:
Stalberg Jonathan
2023-04-14 18:15:06 +02:00
parent 61e732e941
commit 830879cbe6
3 changed files with 61 additions and 35 deletions
Download Patch File Download Diff File Expand all files Collapse all files

78
grum/BECAdapter.py
View File

@ -5,6 +5,8 @@ from os import listdir
from os.path import isfile, join
import h5py
import time
import numpy as np
from PIL import Image
class BECAdapter:
@ -16,8 +18,8 @@ class BECAdapter:
# self.file_reader = .... # add file reader here
self.grum_client = RPCClient("localhost", 8000) # this is outgoing
self.last_plotted_scan_nr = 6755
self.scan_nr = 6757
self.last_plotted_scan_nr = 6760
self.scan_nr = None
def start(self):
self.start_scan_status_sub()
@ -52,47 +54,59 @@ class BECAdapter:
# point = [2, 3]
# self.grum_client.append_data(name, point)
def get_data_from_file(self):
def plot_img_from_h5(self):
while True:
print('checking for new scan_nr')
self.check_for_new_scan_nr()
print('update for new scan_nr')
self.update_scan_nr()
if self.scan_nr > self.last_plotted_scan_nr:
scan = "S0" + str(self.last_plotted_scan_nr + 1)
mypath = "/sls/X12SA/data/e20632/Data10/analysis/S06000-06999/" + scan
# mypath = "/home/stalbe_j/Documents" # for test on own computer
files = [f for f in listdir(mypath) if isfile(join(mypath, f))]
print(files)
recon_files = []
while not recon_files:
recon_files = [
file for file in files if file.endswith("recons.h5")]
print('this are recon_files: ', recon_files)
if recon_files:
break
print('sleeping 1')
time.sleep(10)
# scan = "S0" + str(self.last_plotted_scan_nr + 1)
ending_path = self._get_scan_dir(1000, self.last_plotted_scan_nr + 1, leading_zeros = 5)
mypath = "/sls/X12SA/data/e20632/Data10/analysis/" + ending_path
files = [f for f in listdir(mypath) if isfile(join(mypath, f))]
recon_files = [
file for file in files if file.endswith("recons.h5")]
hf = h5py.File(mypath + '/' + recon_files[0], 'r')
print(hf.keys())
recon = hf.get('reconstruction')
print(recon.keys())
recon_object = hf.get('reconstruction/object')
recon_probes = hf.get('reconstruction/probes')
print(recon_object)
print(recon_probes)
recon_probes_1 = recon_probes[0]
recon_probes_2 = recon_probes[1]
recon_object =np.array(recon_object)
recon_object_abs = np.abs(recon_object)
recon_object_angle = np.angle(recon_object)
# PLOT self.grum_client.new_image(self.last_plotted_scan_nr+1, {'img': recon_object})
self.last_plotted_scan_nr +=1
recon_img_abs = recon_object_abs.tolist()
recon_img_angle = recon_object_angle.tolist()
print('sleeping 2')
time.sleep(5)
# PLOT
self.grum_client.new_image("Absorption", {'image': recon_img_abs, "xlabel": str(self.scan_nr)})
self.grum_client.new_image("Phase", {'image': recon_img_angle, "xlabel": str(self.scan_nr), "colormap":"CET-C1"})
def check_for_new_scan_nr(self):
print('From checking: ')
print('scan_nr: ', self.scan_nr)
print('last_plotted_scan_nr: ', self.last_plotted_scan_nr)
self.last_plotted_scan_nr = self.scan_nr
time.sleep(10)
def update_scan_nr(self):
# return (self.last_plotted_scan_nr == self.scan_nr)
mypath = '/sls/X12SA/Data10/e20632/analysis/online/ptycho/gallery'
file_list = listdir(mypath)
scans = [file_name.split('_')[0] for file_name in file_list]
max_scan_nr = max([int(scan[1:6]) for scan in scans])
print(max_scan_nr)
self.scan_nr = max_scan_nr
def _get_scan_dir(self, scan_bundle, scan_number, leading_zeros=None):
if leading_zeros is None:
leading_zeros = len(str(scan_bundle))
floor_dir = scan_number // scan_bundle * scan_bundle
return f"S{floor_dir:0{leading_zeros}d}-{floor_dir+scan_bundle-1:0{leading_zeros}d}/S{scan_number:0{leading_zeros}d}"
if __name__ == "__main__":
@ -102,4 +116,4 @@ if __name__ == "__main__":
redis_connector = RedisConnector(redis_url)
ba = BECAdapter(redis_connector)
ba.start()
ba.get_data_from_file()
ba.plot_img_from_h5()

15
grum/imgdesc.py
View File

@ -1,14 +1,16 @@
import numpy as np
import pyqtgraph as pg
class ImageDescription:
def __init__(self, name, title=None, xlabel=None, ylabel=None, image=None):
def __init__(self, name, title=None, xlabel=None, ylabel=None, image=None, colormap=None):
self.name = name
self.title = title
self.xlabel = xlabel
self.ylabel = ylabel
self.image = image
self.colormap = colormap
@property
def data(self):
@ -28,16 +30,23 @@ class ImageDescription:
def make_plot(self, plotwidget, style):
res = plotwidget.setImage(self.data)
# plotwidget.colormap()
if self.title:
plotwidget.setTitle(self.title)
if self.xlabel:
plotwidget.setLabel("bottom", self.xlabel)
# vbox = plotwidget.getView()
# vbox.addItem(pg.LabelItem(self.xlabel))
plotwidget.setHistogramLabel(self.xlabel)
# plotwidget.setLabel("bottom", self.xlabel)
if self.ylabel:
plotwidget.setLabel("left", self.ylabel)
if self.colormap:
cm = pg.colormap.get(self.colormap)
plotwidget.setColorMap(cm)
return res

3
grum/mdi/mdisubimg.py
View File

@ -15,6 +15,9 @@ class MDISubImage(MDISubWindow):
style = pg_plot_style()
# cm = pg.colormap.get('CET-C1')
# pw.setColorMap(cm)
plot = desc.make_plot(self.pw, style)
self.plots = {name: plot}