added possibility to plot multiple images

grum/BECAdapter.py

@@ -26,7 +26,7 @@ class BECAdapter:
         self.scan_nr = None 
         self.scan_running = False
 
-        self.eaccount = "e20642" # for jeff: 20633
+        self.eaccount = "e20633" # for jeff: 20633
 
         # To decide what should be plotted
         self.monitor = monitor
@@ -114,13 +114,17 @@ class BECAdapter:
                 self.grum_client_monitor.append_data( "monitor", point)
 
     def plot_img_from_h5(self):
+        
         while True:
             
             # if self.last_plotted_scan_nr !=0:
             print('Check for new reconstruction')
-            self.update_latest_reconstructed()
+            self.update_latest_reconstructed() # uncomment for it to work properly
+            # self.latest_reconstructed += 4
+
             print('latest_reconstructed: ', self.latest_reconstructed)
             print("last plotted scan nr: ", self.last_plotted_scan_nr)
+            
             if self.latest_reconstructed > self.last_plotted_scan_nr:
              
                 ending_path = self._get_scan_dir(1000, self.latest_reconstructed, leading_zeros = 5)
@@ -139,6 +143,8 @@ class BECAdapter:
                 self.last_plotted_scan_nr = self.latest_reconstructed
 
             time.sleep(10)
+            # if self.latest_reconstructed > 9245:
+            #     break 
     def get_recon_file(self, mypath):   
         files = [f for f in listdir(mypath) if isfile(join(mypath, f))]
         for file in files:

grum/mainwin.py

@@ -4,10 +4,11 @@ import pyqtgraph as pg
 
 from . import assets
 from .dictlist import DictList
+from .dictlist.dictlistitem import DictListItem
 from .exampledata import exampledata
 from .h5filedlg import open_h5_files_dialog, save_h5_file_dialog
 from .io import write_dict, read_dict
-from .mdi import MDIArea, MDISubMultiPlot, MDISubPlot, MDISubImage, MDIWindowMode
+from .mdi import MDIArea, MDISubMultiPlot, MDISubPlot, MDISubImage, MDIWindowMode, MDISubMultiImage
 from .menus import BarMenu
 from .plotdesc import PlotDescription
 from .imgdesc import ImageDescription
@@ -93,6 +94,7 @@ class MainWindow(QMainWindow):
             rst.server.register_function(self.extend_data)
             rst.server.register_function(self.set_data)
             rst.server.register_function(self.new_image)
+            rst.server.register_function(self.plot_images_from_list) # function for CSAXS beamtime
 
         self.sig_make_new_plot.connect(self.on_make_new_plot)
         self.sig_make_new_image.connect(self.on_make_new_image)
@@ -116,46 +118,7 @@ class MainWindow(QMainWindow):
             if not self.mdi.findSubWindow(name):
                 self.sig_make_new_plot.emit(name, desc)
 
-            # else:
+    def append_data(self, name, point):
-            #     print("else")
-                # if desc.title:
-
-                #     print("---------------------------------------------")
-                #     print("self mdi exist, new title:", desc.title)    
-                #     sub = self.mdi.findSubWindow(name)
-                #     print(sub.pw.plotItem.titleLabel)
-                #     print(sub.pw.plotItem.titleLabel.text)
-                #     vbox = sub.pw.getViewBox()
-                #     vbox.removeItem(sub.pw.plotItem.titleLabel)
-                #     #maybe add title? or just settitle?
-                #     vbox.addItem(pg.LabelItem(desc.title, size='50pt'))
-                #     # sub.pw.plotItem.titleLabel.setText(desc.title)
-                #     print("------------------------------------")
-                    
-                    # print("clearing")
-                #     if desc.title:
-                #         sub.pw.clear()
-                #         print("setting new title: ", desc.title)
-                #         sub.pw.setTitle(desc.title)
-                #     vbox = sub.pw.getView()  
-                #     vbox.addItem(pg.LabelItem(desc.title, size='50pt'))
-                #     vbox.addItem(pg.titel)
-
-                    # allchildren = vbox.allChildren()
-                    # for child in allchildren: 
-                    #     print(child)
-                    #     if isinstance(child, pg.graphicsItems.ViewBox.ChildGroup):
-                    #         print("Found childGroup")
-                    #         allgrandchildren = vbox.allChildren(child)
-                    #         for grandchild in allgrandchildren:
-                    #             print(grandchild)
-                    #         # print("Removing label")
-                    #         # vbox.removeItem(child)
-                    #     print("-------------done-------------")    
-                    # vbox.addItem(pg.LabelItem(desc.title, size='50pt'))
-                    # sub.pw.setTitle(desc.title)
-
-    def append_data(self, name, point): #, title=None):
         """
         Append a new data point <point> to the (existing) plot <name>.
         The point is forwarded to the append method of PlotDescription.
@@ -163,8 +126,6 @@ class MainWindow(QMainWindow):
         item = self.lst.get(name)
         desc = item.value
         desc.append(point)
-        # if title:
-        #     desc.changeTitle(title)
         self.sync_item_and_plots(item)
 
     def extend_data(self, name, data):
@@ -208,6 +169,21 @@ class MainWindow(QMainWindow):
             else:
                 self.sig_make_new_image.emit(name, desc)
 
+    def plot_images_from_list(self, image_desc_list):
+        """
+        Plot images from list
+        """
+        images = []
+        i =1
+        for img in image_desc_list:
+            self.new_image(img[0], img[1])
+            # desc = ImageDescription(img[0], **img[1])
+            # dlistitem = DictListItem(f"Phase: {i}", desc)
+            # images.append(dlistitem)
+            # i+=1
+
+        # self.plot_multiple_images(images)
+
 
     # Signal callbacks
 
@@ -227,6 +203,8 @@ class MainWindow(QMainWindow):
         if len(selected) == 1:
             item = selected[0]
             self.plot_single_item(item)
+        elif type(selected[0].value) == ImageDescription:
+            self.plot_multiple_images(selected)
         else:
             self.plot_multiple_items(selected)
 
@@ -310,6 +288,23 @@ class MainWindow(QMainWindow):
         name = " | ".join(names)
         self.activate_or_make_subwin(MDISubMultiPlot, name, descs)
 
+    def plot_multiple_images(self, images):
+        if type(images[0])  == list:
+            print('it is a list')
+        
+        else:  
+            print("this is imgdesc now: ", images)
+            for i in images:
+                i.timestamps.access.update()
+                i.set_alarm(False)
+
+            descs = {i.key: i.value for i in images}
+        
+            names = descs.keys()
+            name = " | ".join(names)
+            print(names)
+            self.activate_or_make_subwin(MDISubMultiImage, name, descs)    
+
 
     #TODO: the following two could be methods to MDIArea?
 

grum/mdi/__init__.py

@@ -1,6 +1,6 @@
 
 from .mdiarea import MDIArea, MDIWindowMode
 from .mdisubplot import MDISubPlot, MDISubMultiPlot
-from .mdisubimg import MDISubImage
+from .mdisubimg import MDISubImage, MDISubMultiImage
 
 

grum/mdi/mdisubimg.py

@@ -1,12 +1,19 @@
 import pyqtgraph as pg
 from .mdisubwin import MDISubWindow
 from ..theme import pg_plot_style
+from PyQt5.QtWidgets import QMainWindow, QWidget, QPushButton, QGridLayout, QVBoxLayout, QApplication, QSlider
+from PyQt5.QtCore import Qt, QThread, QTimer
+
+class MDISubImageBase(MDISubWindow):
+    def __init__(self, name, *args, **kwargs):
+        super().__init__(name, *args, **kwargs)
 
 
-class MDISubImage(MDISubWindow):
+class MDISubImage(MDISubImageBase):
 
     def __init__(self, name, desc, *args, **kwargs):
         super().__init__(name, *args, **kwargs)
+        
         self.pw = pw = pg.ImageView()
         self.setWidget(pw)
 
@@ -14,7 +21,6 @@ class MDISubImage(MDISubWindow):
         pw.scene.sigMouseMoved.connect(self.on_hover)
 
         style = pg_plot_style()
-
         # cm = pg.colormap.get('CET-C1')
         # pw.setColorMap(cm)
 
@@ -23,7 +29,6 @@ class MDISubImage(MDISubWindow):
 
         self.image = desc.data
 
-
     def on_hover(self, event):
         coord = self.pw.imageItem.mapFromScene(event)
         x = coord.x()
@@ -38,4 +43,52 @@ class MDISubImage(MDISubWindow):
         self.setToolTip(f"x = {x}\ny = {y}\nz = {z}")
 
 
+class MDISubMultiImage(MDISubImageBase):
 
+    def __init__(self, name, descs, *args, **kwargs):
+        super().__init__(name, *args, **kwargs)
+        self.central_widget = QWidget()
+
+        # self.layout = QGridLayout()
+
+        self.button_next = QPushButton('Next', self.central_widget)
+        self.button_previous = QPushButton('Previous', self.central_widget)
+        self.pw = pw = pg.ImageView()
+        self.slider = QSlider(Qt.Horizontal)
+        self.slider.setRange(0,len(descs)-1)
+
+        self.layout = QGridLayout(self.central_widget)
+        self.layout.addWidget(self.button_next,1,2)
+        self.layout.addWidget(self.button_previous, 1,0)
+        self.layout.addWidget(self.pw, 0,0, 1,3)
+        self.layout.addWidget(self.slider, 1,1)
+        self.setWidget(self.central_widget)
+
+        self.button_next.clicked.connect(self.update_img_next)
+        self.button_previous.clicked.connect(self.update_img_previous)
+        self.slider.valueChanged.connect(self.update_img)
+        
+        names = [names for names, _ in descs.items()]
+        self.descriptions = [desc for _, desc in descs.items()]
+
+        desc = self.descriptions[0]
+
+        style = pg_plot_style()
+        plot = desc.make_plot(self.pw, style)
+        self.plots = {name: plot}
+        self.image = desc.data
+
+
+        # self.update_timer = QTimer()
+        # self.update_timer.timeout.connect(self.update_movie)
+
+    def update_img_next(self):
+        self.pw.setImage(self.descriptions[1].data)
+        self.slider.setValue(self.slider.value()+1)
+
+    def update_img_previous(self):
+        self.pw.setImage(self.descriptions[0].data)
+        self.slider.setValue(self.slider.value()-1)
+
+    def update_img(self, value):
+        self.pw.setImage(self.descriptions[value].data)

grum/plot_multiple_phases.py

@@ -0,0 +1,76 @@
+from grum.rpc import RPCClient
+from os import listdir
+from os.path import isfile, join
+import h5py
+import numpy as np
+
+class plotPhases:
+    def __init__(self, start, end, step=1):
+        self.start = start
+        self.end = end
+        self.step =step
+        self.eaccount = "e20633" # for jeff: 20633
+        self.grum_client = RPCClient("localhost", 8000)   # this is outgoing
+        self.image_description_list = [] 
+
+
+    def plot_all_phases(self):
+
+        for scan_nr in range(self.start, self.end + 1, self.step):
+            print("retrieving data for scan: ", scan_nr)
+            ending_path = self._get_scan_dir(1000, scan_nr, leading_zeros = 5)
+            mypath = "/sls/X12SA/data/" + self.eaccount + "/Data10/analysis/" + ending_path           
+            recon_file = self.get_recon_file(mypath)
+            with h5py.File(mypath + '/' + recon_file, 'r') as hf:
+                recon_img_phase = self.get_recon_phase(hf)
+            
+            xlab = str(scan_nr)
+            self.image_description_list.append([f"Phase: {scan_nr}", {'image': recon_img_phase, "xlabel": xlab}])
+
+        print("calling plot images from list")
+        self.grum_client.plot_images_from_list(self.image_description_list)        
+
+    def get_recon_phase(self, hf):
+    
+        recon = hf.get('reconstruction')
+        recon_object = hf.get('reconstruction/object')
+        # recon_probes = hf.get('reconstruction/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)
+        
+        # recon_object_abs = np.rot90(recon_object_abs,3)
+        recon_object_angle = np.rot90(recon_object_angle, 3)
+
+        # recon_img_abs = recon_object_abs.tolist()
+        recon_img_angle = recon_object_angle.tolist()
+        # return recon_img_abs, recon_img_angle
+        return recon_img_angle
+    
+    def get_recon_file(self, mypath):   
+        files = [f for f in listdir(mypath) if isfile(join(mypath, f))]
+        for file in files:
+            if file.endswith("recons.h5"):
+                return file
+        print("no file fro this scan nr")        
+        return None
+    
+    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__":
+    start = 10296
+    end = 10300
+    step = 1
+    print('starts plotting phase for scans: ',start, ' to ', end)
+    
+    pp = plotPhases(start, end)
+    pp.plot_all_phases()

setup.py

@@ -12,7 +12,7 @@ if __name__ == "__main__":
     # subprocess.run(f"pip install -e {bec_utils}", shell=True, check=True)
 
     setup(
-        install_requires=["pyqt5==5.12", "pyqtgraph", "h5py", "PyQtWebEngine==5.12"], #this version works for comp1 CSAXS, no later version
+        install_requires=["pyqt5==5.12", "pyqtgraph", "h5py", "PyQtWebEngine==5.12", "Pillow"], #this version works for comp1 CSAXS, no later version
         entry_points={"console_scripts": ["grum=grum:main"]},
     )