cleanup after beamtime
This commit is contained in:
e20631
@ -13,29 +13,31 @@ class BECAdapter:
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def __init__(self, redis_connector, recon = False, monitor=False, motor_pos = False) -> None:
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super().__init__()
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self.redis_connector = redis_connector # this is incoming
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# self.file_reader = .... # add file reader here
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self.grum_client_monitor = RPCClient("localhost", 8000) # this is outgoing
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self.grum_client_motor_pos_static = RPCClient("localhost", 8000) # this is outgoing
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self.grum_client_motor_pos_moving = RPCClient("localhost", 8000) # this is outgoing
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self.grum_client_recon_abs = RPCClient("localhost", 8000) # this is outgoing
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self.grum_client_recon_phase = RPCClient("localhost", 8000) # this is outgoing
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self.last_plotted_scan_nr = 0
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self.latest_reconstructed = 5379
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self.scan_nr = None
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self.scan_running = False
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host = "localhost"
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port = 8000
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self.redis_connector = redis_connector
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self.eaccount = "e20631" #change for each new beamtime
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# To decide what should be plotted
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self.monitor = monitor
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self.motor_pos = motor_pos
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self.recon = recon
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if self.recon:
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self.grum_client_recon_abs = RPCClient(host, port)
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self.grum_client_recon_phase = RPCClient(host, port)
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self.last_plotted_scan_nr = 0
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self.latest_reconstructed = 5000
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if self.monitor:
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self.grum_client_monitor.new_plot( "monitor",{'xlabel':'time', 'ylabel':"sls_ring_current", "time": True, "frmt":"Line" })
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self.grum_client_monitor = RPCClient(host ,port)
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self.grum_client_monitor.new_plot("monitor",{'xlabel':'time', 'ylabel':"sls_ring_current", "time": True, "frmt":"Line" })
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if self.motor_pos:
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self.grum_client_motor_pos_static = RPCClient(host, port)
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self.grum_client_motor_pos_moving = RPCClient(host, port)
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self.scan_nr = None
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self.scan_running = False
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self.grum_client_motor_pos_static.new_plot("Motor position static", {'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp" , "frmt": "Dots"})
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self.grum_client_motor_pos_moving.new_plot("Motor position move", {'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp" , 'frmt':"Motor pos move"})
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@ -116,38 +118,26 @@ class BECAdapter:
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def plot_img_from_h5(self):
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while True:
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# if self.last_plotted_scan_nr !=0:
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print('Check for new reconstruction')
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self.update_latest_reconstructed() # uncomment for it to work properly
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# self.latest_reconstructed += 4
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self.update_latest_reconstructed()
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print('latest_reconstructed: ', self.latest_reconstructed)
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print("last plotted scan nr: ", self.last_plotted_scan_nr)
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if self.latest_reconstructed > self.last_plotted_scan_nr:
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ending_path = self._get_scan_dir(1000, self.latest_reconstructed, leading_zeros = 5)
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mypath = "/sls/X12SA/data/" + self.eaccount + "/Data10/analysis/" + ending_path
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recon_file = self.get_recon_file(mypath)
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with h5py.File(mypath + '/' + recon_file, 'r') as hf:
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recon_img_abs, recon_img_phase = self.get_recon_imgs(hf)
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# PLOT
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# print("max(recon_img_abs)", max(max(recon_img_abs)))
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# print("max(recon_img_phase)", max(max(recon_img_phase)))
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print('plotting new image with scan_nr: ', self.latest_reconstructed)
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xlab = str(self.latest_reconstructed)
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if self.recon:
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self.grum_client_recon_abs.new_image( "Absorption", {'image': recon_img_abs, "xlabel": xlab, "levels":[0.9, 1.1]})
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self.grum_client_recon_abs.new_image( "Absorption", {'image': recon_img_abs, "xlabel": xlab}) #, "levels":[0.9, 1.1]})
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# self.grum_client_recon_phase.new_image( f"Phase for scan_nr: {self.latest_reconstructed}", {'image': recon_img_angle, "xlabel": xlab}) #, "colormap":"CET-C1"})
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self.grum_client_recon_phase.new_image( "Phase", {'image': recon_img_phase, "xlabel": xlab, "levels": [-1,1]}) #, "colormap":"CET-C1"})
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self.grum_client_recon_phase.new_image( "Phase", {'image': recon_img_phase, "xlabel": xlab})#, "levels": [-1,1]}) #, "colormap":"CET-C1"})
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self.last_plotted_scan_nr = self.latest_reconstructed
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time.sleep(10)
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# if self.latest_reconstructed > 9245:
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# break
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def get_recon_file(self, mypath):
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files = [f for f in listdir(mypath) if isfile(join(mypath, f))]
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for file in files:
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@ -156,12 +146,8 @@ class BECAdapter:
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return None
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def get_recon_imgs(self, hf):
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recon = hf.get('reconstruction')
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recon_object = hf.get('reconstruction/object')
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recon_probes = hf.get('reconstruction/probes')
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recon_probes_1 = recon_probes[0]
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recon_probes_2 = recon_probes[1]
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# recon_probes = hf.get('reconstruction/probes')
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recon_object =np.array(recon_object)
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recon_object_abs = np.abs(recon_object)
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@ -175,11 +161,11 @@ class BECAdapter:
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return recon_img_abs, recon_img_phase
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def update_latest_reconstructed(self):
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mypath = '/sls/X12SA/Data10/' + self.eaccount + '/analysis/online/ptycho/gallery'
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# mypath = '/sls/X12SA/Data10/' + self.eaccount + '/analysis/online/ptycho/gallery'
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mypath = '/sls/X12SA/data/' +self.eaccount+ '/Data10/specES1/ptycho_reconstruct/done' # ptycho_reconstruct argument?
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file_list = listdir(mypath)
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scans = [file_name.split('_')[0] for file_name in file_list]
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self.latest_reconstructed = max([int(scan[1:6]) for scan in scans])
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# print('Latest reconstructed: ', self.latest_reconstructed)
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scans = [file_name.split('_')[1] for file_name in file_list] #0 if you do gallery, 1 if you do done
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self.latest_reconstructed = max([int(scan[0:5]) for scan in scans]) # 1:6 for gallery, 0:5 for done
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def _get_scan_dir(self, scan_bundle, scan_number, leading_zeros=None):
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if leading_zeros is None:
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@ -187,7 +173,6 @@ class BECAdapter:
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floor_dir = scan_number // scan_bundle * scan_bundle
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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}"
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if __name__ == "__main__":
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print('starts BECAdapter')
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print("initializing redis-connector")
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@ -14,6 +14,7 @@ class ImageDescription:
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self.image = image
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self.colormap = colormap
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self.levels = levels
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@property
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def data(self):
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return np.asarray(self.image)
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@ -22,7 +23,6 @@ class ImageDescription:
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def data(self, value):
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self.image = value
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def append(self, xy):
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print("ignored image append")
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@ -32,10 +32,10 @@ class ImageDescription:
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def make_plot(self, plotwidget, style):
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if self.levels:
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res = plotwidget.setImage(self.data, levels = self.levels)
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res = plotwidget.setImage(self.data, levels = self.levels) #Set levels for histogram
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else:
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res = plotwidget.setImage(self.data)
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# plotwidget.colormap()
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if self.title:
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plotwidget.setTitle(self.title)
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@ -170,9 +170,6 @@ class MainWindow(QMainWindow):
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self.sig_make_new_image.emit(name, desc)
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def append_image_to_list(self, img):
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"""
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Append image to list
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"""
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desc = self.add_new_desc_to_list(img[0], img[1], Desc=ImageDescription)
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# Signal callbacks
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@ -193,7 +190,7 @@ class MainWindow(QMainWindow):
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if len(selected) == 1:
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item = selected[0]
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self.plot_single_item(item)
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elif type(selected[0].value) == ImageDescription:
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elif type(selected[0].value) == ImageDescription: #TODO: what should be the typecheck?
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self.plot_multiple_images(selected)
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else:
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self.plot_multiple_items(selected)
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@ -280,19 +277,14 @@ class MainWindow(QMainWindow):
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def plot_multiple_images(self, images):
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print("this is imgdesc now: ", images)
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for i in images:
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i.timestamps.access.update()
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i.set_alarm(False)
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descs = {i.key: i.value for i in images}
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names = descs.keys()
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name = " | ".join(names)
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print(names)
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self.activate_or_make_subwin(MDISubMultiImage, name, descs)
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#TODO: the following two could be methods to MDIArea?
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def activate_or_make_subwin(self, MDISubType, name, *args, **kwargs):
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@ -15,8 +15,6 @@ class MDISubImage(MDISubImageBase):
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super().__init__(name, *args, **kwargs)
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self.pw = pw = pg.ImageView()
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# self.pw.setLevels(1,2) # changing levels for histogram levels colors
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# self.pw.getHistogramWidget().setLevels(500, 501)
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self.setWidget(pw)
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# connect to plot mouse-over event
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@ -28,7 +26,6 @@ class MDISubImage(MDISubImageBase):
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plot = desc.make_plot(self.pw, style)
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self.plots = {name: plot}
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self.image = desc.data
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def on_hover(self, event):
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@ -49,18 +46,28 @@ class MDISubMultiImage(MDISubImageBase):
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def __init__(self, name, descs, *args, **kwargs):
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super().__init__(name, *args, **kwargs)
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self.pw = pw = pg.ImageView()
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self.central_widget = QWidget()
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# self.layout = QGridLayout()
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self.button_next = QPushButton('Next', self.central_widget)
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self.button_previous = QPushButton('Previous', self.central_widget)
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self.pw = pw = pg.ImageView()
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self.slider = QSlider(Qt.Horizontal)
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self.slider.setRange(0,len(descs)-1)
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self._create_layout()
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self._connect_signals()
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names = [names for names, _ in descs.items()]
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self.descriptions = [desc for _, desc in descs.items()]
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desc = self.descriptions[0]
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style = pg_plot_style()
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plot = desc.make_plot(self.pw, style)
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self.plots = {name: plot}
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self.image = desc.data
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def _create_layout(self):
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self.layout = QGridLayout(self.central_widget)
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self.layout.addWidget(self.button_next,1,2)
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self.layout.addWidget(self.button_previous, 1,0)
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@ -68,45 +75,23 @@ class MDISubMultiImage(MDISubImageBase):
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self.layout.addWidget(self.slider, 1,1)
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self.setWidget(self.central_widget)
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self.button_next.clicked.connect(self.update_img_next)
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self.button_previous.clicked.connect(self.update_img_previous)
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def _connect_signals(self):
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self.button_next.clicked.connect(lambda:self.update_slider(1))
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self.button_previous.clicked.connect(lambda:self.update_slider(-1))
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self.slider.valueChanged.connect(self.update_img)
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names = [names for names, _ in descs.items()]
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self.descriptions = [desc for _, desc in descs.items()]
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desc = self.descriptions[0]
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plot = desc.make_plot(self.pw, style)
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self.plots = {name: plot}
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self.image = desc.data
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# self.update_timer = QTimer()
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# self.update_timer.timeout.connect(self.update_movie)
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def update_img_next(self):
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self.slider.setValue(self.slider.value()+1)
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self.pw.setImage(self.descriptions[self.slider.value()].data)
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self.set_title()
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def update_img_previous(self):
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self.slider.setValue(self.slider.value()-1)
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self.pw.setImage(self.descriptions[self.slider.value()].data)
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self.set_title()
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def update_slider(self, value):
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self.slider.setValue(self.slider.value()+value)
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def update_img(self, value):
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self.pw.setImage(self.descriptions[value].data)
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self.set_title()
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self.set_title_in_image()
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def set_title(self):
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vbox = self.pw.getView()
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allchildren = vbox.allChildren()
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for child in allchildren:
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if isinstance(child, pg.LabelItem):
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vbox.removeItem(child)
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vbox.addItem(pg.LabelItem(self.descriptions[self.slider.value()].xlabel, size='50pt'))
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def set_title_in_image(self):
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if self.descriptions[self.slider.value()].xlabel:
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vbox = self.pw.getView()
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allchildren = vbox.allChildren()
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for child in allchildren:
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if isinstance(child, pg.LabelItem):
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vbox.removeItem(child)
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vbox.addItem(pg.LabelItem(self.descriptions[self.slider.value()].xlabel, size='50pt'))
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@ -6,14 +6,16 @@ import numpy as np
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import argparse
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class plotPhases:
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"""
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A possibility to plot reconstructions in a scan number range
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"""
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def __init__(self, start, end, step=1):
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self.start = start
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self.end = end
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self.step =step
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self.eaccount = "e20631"
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self.grum_client = RPCClient("localhost", 8000) # this is outgoing
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self.image_description_list = []
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# self.image_description_list = []
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def plot_all_phases(self):
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@ -35,7 +37,6 @@ class plotPhases:
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def get_recon_phase(self, hf):
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recon = hf.get('reconstruction')
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recon_object = hf.get('reconstruction/object')
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recon_object = np.array(recon_object)
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@ -50,7 +51,7 @@ class plotPhases:
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for file in files:
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if file.endswith("recons.h5"):
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return file
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print("no file fro this scan nr")
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print("no file for this scan nr")
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return None
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def _get_scan_dir(self, scan_bundle, scan_number, leading_zeros=None):
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@ -61,19 +62,17 @@ class plotPhases:
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if __name__ == "__main__":
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start = 10296
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end = 10300
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start = 5037 # default
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end = 5038 # default
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step = 1
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parser = argparse.ArgumentParser(description="description", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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parser.add_argument("-s", "--startstop", nargs =2, help="set start, end")
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parser.add_argument("-s", "--startend", nargs =2, help="set start, end")
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clargs = parser.parse_args()
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if clargs:
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start = int(clargs.startstop[0])
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end = int(clargs.startstop[1])
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start = int(clargs.startend[0])
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end = int(clargs.startend[1])
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print('starts plotting phase for scans: ',start, ' to ', end)
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pp = plotPhases(start, end)
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pp.plot_all_phases()
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@ -1,88 +0,0 @@
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from abc import ABC, abstractmethod
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from bec_utils import BECMessage, MessageEndpoints
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from PyQt5.QtCore import QObject, pyqtSignal
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from PyQt5.QtCore import QObject, pyqtSignal
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from bec_utils import BECMessage
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pyqtWrapperType = type(QObject)
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class FinalMeta(pyqtWrapperType, ABC):
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pass
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class ConnectorBase(QObject, metaclass=FinalMeta):
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msg_update = pyqtSignal(BECMessage.ScanStatusMessage)
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@abstractmethod
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def start_scan_sub(self):
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""" """
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class BECConnector(ConnectorBase):
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msg_update = pyqtSignal(BECMessage.ScanStatusMessage)
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def __init__(self, redis_connector) -> None:
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super().__init__()
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self.connector = redis_connector
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self.producer = self.connector.producer()
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self._scan_sub = None
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def start_scan_sub(self):
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self._scan_sub = self.connector.consumer(
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MessageEndpoints.scan_status(), cb=self.scan_status_update, parent=self
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)
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self._scan_sub.start()
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@staticmethod
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def scan_status_update(msg, parent):
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# print("scan_status_update", msg)
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msg = BECMessage.ScanStatusMessage.loads(msg.value)
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parent.msg_update.emit(msg)
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class DataAccess(QObject):
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new_mon_value = pyqtSignal(str)
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used_devices_updated = pyqtSignal(bool)
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new_scan_started = pyqtSignal(bool)
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new_scan_msg = pyqtSignal(BECMessage.BECMessage)
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msg_queue_update = pyqtSignal(BECMessage.BECMessage)
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new_position_umv = pyqtSignal(bool)
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def __init__(self, connector: ConnectorBase):
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super().__init__()
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self.connector = connector
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self.start_all_subscriptions(self.connector)
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self.scan_nr = ""
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self.connect_pyqtSignals()
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print('data_access initialized')
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||||
|
||||
def start_all_subscriptions(self, conn):
|
||||
conn.start_scan_sub()
|
||||
|
||||
def on_msg_update(self, msg: BECMessage.ScanStatusMessage):
|
||||
"""
|
||||
This function is run whenever there is a new message.
|
||||
Args:
|
||||
msg (BECMessage.ScanStatusMessage): A scan status message
|
||||
"""
|
||||
print("on_msg_update called")
|
||||
if msg.content["status"] == "open":
|
||||
self.get_scan_info(msg)
|
||||
# self.reset_plot_data()
|
||||
self.new_scan_started.emit(True)
|
||||
else:
|
||||
print("scan ended")
|
||||
|
||||
def get_scan_info(self, msg):
|
||||
print(
|
||||
"--------------------------------------------------------------------------------------------"
|
||||
)
|
||||
print("New scan started")
|
||||
self.scan_nr = msg.content["info"]["scan_number"]
|
||||
print(
|
||||
"--------------------------------------------------------------------------------------------"
|
||||
)
|
||||
|
||||
def connect_pyqtSignals(self):
|
||||
self.connector.msg_update.connect(self.on_msg_update)
|
||||
|
||||
|
||||
|
||||
@ -21,28 +21,19 @@ class PlotDescription:
|
||||
def data(self, value):
|
||||
self.xs, self.ys = value
|
||||
|
||||
|
||||
def append(self, xy):
|
||||
x, y = xy
|
||||
self.xs.append(x)
|
||||
self.ys.append(y)
|
||||
|
||||
# def changeTitle(self, title):
|
||||
# self.title = title
|
||||
|
||||
def extend(self, data):
|
||||
xs, ys = data
|
||||
self.xs.extend(xs)
|
||||
self.ys.extend(ys)
|
||||
|
||||
|
||||
def make_plot(self, plotwidget, style):
|
||||
if self.format == "Line":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen="w") #, **style)
|
||||
elif self.format == "Dots":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen=None, symbol="o", symbolSize = 5) #, **style)
|
||||
elif self.format == "Motor pos move":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen='r', symbol="o", symbolSize = 10)
|
||||
if self.format:
|
||||
res = plot_with_format()
|
||||
else:
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, **style)
|
||||
|
||||
@ -61,9 +52,15 @@ class PlotDescription:
|
||||
|
||||
return res
|
||||
|
||||
|
||||
def to_dict(self):
|
||||
return {k: v for k, v in self.__dict__.items() if not k.startswith("_") and k != "name" and v is not None}
|
||||
|
||||
|
||||
|
||||
def plot_with_format():
|
||||
if self.format == "Line":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen="w")
|
||||
elif self.format == "Dots":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen=None, symbol="o", symbolSize = 5)
|
||||
elif self.format == "Motor pos move":
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, pen='r', symbol="o", symbolSize = 10)
|
||||
else:
|
||||
res = plotwidget.plot(self.xs, self.ys, name=self.name, **style)
|
||||
|
||||
Reference in New Issue
Block a user