changes at beamline

grum/BECAdapter.py

@@ -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
+                # 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))]
-                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)
    
                 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)
 
-                # PLOT self.grum_client.new_image(self.last_plotted_scan_nr+1, {'img': recon_object})
-                self.last_plotted_scan_nr +=1
+                recon_probes_1 = recon_probes[0]
+                recon_probes_2 = recon_probes[1]
 
-            print('sleeping 2')
-            time.sleep(5)
+                recon_object =np.array(recon_object)
+                recon_object_abs = np.abs(recon_object)
+                recon_object_angle = np.angle(recon_object)
                 
-    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)
+                recon_img_abs = recon_object_abs.tolist()
+                recon_img_angle = recon_object_angle.tolist()
+
+                # 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"})
+
+                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()

grum/imgdesc.py

@@ -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
 
 

grum/mdi/mdisubimg.py

@@ -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}