get list names, thoughts about multiplotting

.gitlab-ci.yml

@@ -6,7 +6,7 @@ stages:
   - pip install pytest pytest-random-order pytest-cov
   - pip install -e ./
   - apt-get update
-  - apt-get install -y ffmpeg libnss3 libxcomposite1 libxtst6 libxdamage1
+  - apt-get install -y ffmpeg libnss3 libxcomposite1 libxtst6
 
 tests:
   stage: Tests
@@ -24,10 +24,8 @@ tests:
   artifacts:
     when: always
     reports:
-      junit: report.xml
-      coverage_report:
-        coverage_format: cobertura
-        path: coverage.xml
+      cobertura: coverage.xml
+      junit: report-junit.xml
 
 tests-3.6:
   stage: OptionalTests

README.md

@@ -1,6 +1,6 @@
 # grum
 
-<img src="https://gitea.psi.ch/SwissFEL/grum/wiki/raw/uploads%2Fe4cd2be847d26bb7ac7100080edbccce%2Fscreenshot.png" width="50%" />
+<img src="https://gitlab.psi.ch/augustin_s/grum/-/wikis/uploads/1a259a1d74e7b79e0230e7bbad3b1284/screenshot2.png" width="50%" />
 
 ## Overview
 
@@ -22,11 +22,11 @@ Via the RPC server, new plots can be created and new data appended to existing p
 
 - `new_plot(name, cfg)`
 
-Creates a new plot named `name` in the grum list. The configuration dict `cfg` is used as arguments for the constructor of [`PlotDescription`](https://gitea.psi.ch/SwissFEL/grum/src/grum/descs/plotdesc.py#L4).
+Creates a new plot named `name` in the grum list. The configuration dict `cfg` is used as arguments for the constructor of [`PlotDescription`](https://gitlab.psi.ch/augustin_s/grum/-/blob/master/grum/plotdesc.py#L4).
 
 - `append_data(name, point)`
 
-Append data point to the plot named `name`. The new `point` is forwarded to [`PlotDescription.append()`](https://gitea.psi.ch/SwissFEL/grum/src/grum/descs/plotdesc.py#L24).
+Append data point to the plot named `name`. The new `point` is forwarded to [`PlotDescription.append()`](https://gitlab.psi.ch/augustin_s/grum/-/blob/master/grum/plotdesc.py#L18).
 
 ### Utility functions
 

grum/BECAdapter.py

@@ -0,0 +1,183 @@
+from grum.rpc import RPCClient
+from bec_utils import BECMessage, MessageEndpoints
+from bec_utils import RedisConnector
+from os import listdir
+from os.path import isfile, join
+import h5py
+import time
+import numpy as np
+from PIL import Image
+
+class BECAdapter:
+
+    def __init__(self, redis_connector, recon = False, monitor=False, motor_pos = False) -> None:
+        super().__init__()
+
+        host = "localhost"
+        port = 8000
+        self.redis_connector = redis_connector
+        self.eaccount = "e20631" #change for each new beamtime
+
+        # To decide what should be plotted
+        self.monitor = monitor
+        self.motor_pos = motor_pos
+        self.recon = recon
+        
+        if self.recon:
+            self.grum_client_recon_abs = RPCClient(host, port)  
+            self.grum_client_recon_phase = RPCClient(host, port)   
+            self.last_plotted_scan_nr = 0
+            self.latest_reconstructed = 5000        
+
+        if self.monitor:
+            self.grum_client_monitor = RPCClient(host ,port)
+            self.grum_client_monitor.new_plot("monitor",{'xlabel':'time', 'ylabel':"sls_ring_current", "time": True, "frmt":"Line" })
+
+        if self.motor_pos:
+            self.grum_client_motor_pos_static = RPCClient(host, port)  
+            self.grum_client_motor_pos_moving = RPCClient(host, port)   
+            self.scan_nr = None 
+            self.scan_running = False
+            self.grum_client_motor_pos_static.new_plot("Motor position static", {'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp" , "frmt": "Dots"})
+            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"})
+
+    def start(self):
+        if self.motor_pos:
+            self.start_scan_status_sub()
+            self.start_scan_segment_sub()
+        if self.monitor:
+            self.start_monitor_sub()
+        
+    def start_scan_status_sub(self):
+        self._scan_sub = self.redis_connector.consumer(
+            MessageEndpoints.scan_status(), cb=self.scan_status_update
+        )
+        self._scan_sub.start()
+    
+    def scan_status_update(self, segment):
+        # whenever a new scan starts or ends, for now changes scan nr both in start and end
+        segment = BECMessage.ScanStatusMessage.loads(segment.value)
+        if segment.content["status"] == "open":
+            self.scan_nr = segment.content["info"]["scan_number"]
+            self.positions = segment.content["info"]["positions"]
+            self.grum_client_motor_pos_moving.new_plot("Motor position move", {"title":"scan number:" + str(self.scan_nr),'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp" })
+            xpos = [x for x,y in self.positions]
+            ypos = [y for x,y in self.positions]
+            if len(segment.content["info"]["primary"]) == 2:
+                self.scan_running = True
+                if self.motor_pos:
+                    print("new plot")
+                    # for point in self.positions
+                    # self.grum_client_motor_pos_static.append_data("Motor position static", self.positions)
+                    self.grum_client_motor_pos_static.new_plot( "Motor position static", { "xs": xpos, "ys":ypos, 'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp", "frmt": "Dots"})
+                    #Trying to update plots with "open new plots" unticked 
+                    # self.grum_client_motor_pos_static.new_plot( "Motor position static", {"xs": xpos[:-1], "ys":ypos[:-1], 'xlabel':'average_x_st_fzp', 'ylabel':"average_y_st_fzp", "frmt": "Dots"})
+                    # self.grum_client_motor_pos_static.append_data( "Motor position static", [xpos[-1], ypos[-1]] )
+
+            else:
+                self.scan_running = False
+
+            if len(segment.content["info"]["primary"]) == 1:
+                print("umv")
+        
+    def start_scan_segment_sub(self):
+        self._scan_segment_sub = self.redis_connector.consumer(
+            MessageEndpoints.scan_segment(), cb=self.scan_segment_update
+        )
+        self._scan_segment_sub.start()
+
+
+    def scan_segment_update(self, segment):
+        if self.scan_running:
+            segment = BECMessage.ScanMessage.loads(segment.value)
+            x_val = segment[0].content["data"]["average_x_st_fzp"]["value"]
+            y_val = segment[0].content["data"]["average_y_st_fzp"]["value"]
+
+            point = [x_val, y_val]
+            if self.motor_pos:
+                self.grum_client_motor_pos_moving.append_data("Motor position move", point)   
+
+    def start_monitor_sub(self):
+        self._monitor_sub = self.redis_connector.consumer(
+            pattern = MessageEndpoints.device_readback('*'), 
+            cb=self.monitor_update
+        )
+        self._monitor_sub.start()
+
+    def monitor_update(self, msg):
+        # Whenever we get a new monitor value
+        dev = msg.topic.decode().split(MessageEndpoints._device_readback + '/')[-1].split(':sub')[0]
+        msg = BECMessage.DeviceMessage.loads(msg.value)
+        if dev == "sls_ring_current":
+            x = msg.content["signals"][dev]['timestamp']
+            y = msg.content["signals"][dev]['value']
+            point = [x,y]
+            if self.monitor:
+                self.grum_client_monitor.append_data( "monitor", point)
+
+    def plot_img_from_h5(self):
+        
+        while True:
+            print('Check for new reconstruction')
+            self.update_latest_reconstructed()
+            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)
+                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_abs, recon_img_phase = self.get_recon_imgs(hf)
+                print('plotting new image with scan_nr: ', self.latest_reconstructed)
+                xlab = str(self.latest_reconstructed)
+                if self.recon:
+                    self.grum_client_recon_abs.new_image( "Absorption", {'image': recon_img_abs, "xlabel": xlab}) #, "levels":[0.9, 1.1]})
+                    # self.grum_client_recon_phase.new_image( f"Phase for scan_nr: {self.latest_reconstructed}", {'image': recon_img_angle, "xlabel": xlab}) #, "colormap":"CET-C1"})
+                    self.grum_client_recon_phase.new_image( "Phase", {'image': recon_img_phase, "xlabel": xlab})#, "levels": [-1,1]}) #, "colormap":"CET-C1"})
+                self.last_plotted_scan_nr = self.latest_reconstructed
+
+            time.sleep(10)
+    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
+        return None
+    
+    def get_recon_imgs(self, hf):   
+        recon_object = hf.get('reconstruction/object')
+        # recon_probes = hf.get('reconstruction/probes')
+
+        recon_object =np.array(recon_object)
+        recon_object_abs = np.abs(recon_object)
+        recon_object_phase = np.angle(recon_object)
+        
+        recon_object_abs = np.rot90(recon_object_abs,3)
+        recon_object_phase = np.rot90(recon_object_phase, 3)
+
+        recon_img_abs = recon_object_abs.tolist()
+        recon_img_phase = recon_object_phase.tolist()
+        return recon_img_abs, recon_img_phase
+   
+    def update_latest_reconstructed(self):
+        # mypath = '/sls/X12SA/Data10/' + self.eaccount + '/analysis/online/ptycho/gallery'
+        mypath = '/sls/X12SA/data/' +self.eaccount+ '/Data10/specES1/ptycho_reconstruct/done' # ptycho_reconstruct argument?
+        file_list = listdir(mypath)
+        scans = [file_name.split('_')[1] for file_name in file_list] #0 if you do gallery, 1 if you do done
+        self.latest_reconstructed = max([int(scan[0:5]) for scan in scans]) # 1:6 for gallery, 0:5 for done
+
+    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__":
+    print('starts BECAdapter')
+    print("initializing redis-connector")
+    redis_url = "129.129.122.75:6379"  # for LamNI
+    redis_connector = RedisConnector(redis_url)
+    ba = BECAdapter(redis_connector, recon=True) #, motor_pos=True)  #, monitor=True)
+    ba.start()
+    ba.plot_img_from_h5()

grum/cli.py

@@ -10,7 +10,7 @@ from .mdi import MDIWindowMode
 
 def main():
     app = QApplication(sys.argv)
-    ctrl_c.setup(app)
+    # ctrl_c.setup(app)
 
     clargs = handle_clargs()
     if not clargs.pop("no_theme"):

grum/ctrl_c.py

@@ -1,10 +1,10 @@
 import signal
 import socket
-from PyQt5.QtNetwork import QAbstractSocket
+# from PyQt5.QtNetwork import QAbstractSocket
 
 
 def setup(app):
-    app.signalwatchdog = SignalWatchdog() # need to store to keep socket pair alive
+    # app.signalwatchdog = SignalWatchdog() # need to store to keep socket pair alive
     signal.signal(signal.SIGINT, make_quit_handler(app))
 
 
@@ -16,25 +16,25 @@ def make_quit_handler(app):
 
 
 
-class SignalWatchdog(QAbstractSocket):
+# class SignalWatchdog(QAbstractSocket):
 
-    def __init__(self):
-        """
-        Propagates system signals from Python to QEventLoop
-        adapted from https://stackoverflow.com/a/65802260/655404
-        """
-        super().__init__(QAbstractSocket.SctpSocket, None)
+#     def __init__(self):
+#         """
+#         Propagates system signals from Python to QEventLoop
+#         adapted from https://stackoverflow.com/a/65802260/655404
+#         """
+#         super().__init__(QAbstractSocket.SctpSocket, None)
 
-        self.writer, self.reader = writer, reader = socket.socketpair()
-        writer.setblocking(False)
+#         self.writer, self.reader = writer, reader = socket.socketpair()
+#         writer.setblocking(False)
 
-        fd_writer = writer.fileno()
-        fd_reader = reader.fileno()
+#         fd_writer = writer.fileno()
+#         fd_reader = reader.fileno()
 
-        signal.set_wakeup_fd(fd_writer) # Python hook
-        self.setSocketDescriptor(fd_reader) # Qt hook
+#         signal.set_wakeup_fd(fd_writer) # Python hook
+#         self.setSocketDescriptor(fd_reader) # Qt hook
 
-        self.readyRead.connect(lambda: None) # dummy function call that lets the Python interpreter run
+#         self.readyRead.connect(lambda: None) # dummy function call that lets the Python interpreter run
 
 
 

grum/descs/__init__.py

@@ -1,13 +0,0 @@
-
-from .desc import Description
-from .imgdesc import ImageDescription
-from .plotdesc import PlotDescription
-
-
-DESC_TYPES = {
-    ImageDescription.get_type(): ImageDescription,
-    PlotDescription.get_type():  PlotDescription
-}
-
-
-

grum/descs/desc.py

@@ -1,23 +0,0 @@
-
-class Description:
-
-    def to_dict(self):
-        res = {k: v for k, v in self.__dict__.items() if not k.startswith("_") and k != "name" and v is not None}
-        tn = self.get_type()
-        res.setdefault("type", tn)
-        return res
-
-
-    @classmethod
-    def get_type(cls):
-        tn = cls.__name__
-        suffix = "Description"
-        if not tn.endswith(suffix):
-            raise ValueError(f'"{tn}" does not end with "{suffix}"')
-        tn = tn[:-len(suffix)]
-        tn = tn.casefold()
-        tn = tn or None
-        return tn
-
-
-

grum/descs/plotdesc.py

@@ -1,50 +0,0 @@
-from .desc import Description
-
-
-class PlotDescription(Description):
-
-    def __init__(self, name, title=None, xlabel=None, ylabel=None, xs=None, ys=None):
-        self.name = name
-        self.title = title
-        self.xlabel = xlabel
-        self.ylabel = ylabel
-        self.xs = [] if xs is None else list(xs)
-        self.ys = [] if ys is None else list(ys)
-
-
-    @property
-    def data(self):
-        return (self.xs, self.ys)
-
-    @data.setter
-    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 extend(self, data):
-        xs, ys = data
-        self.xs.extend(xs)
-        self.ys.extend(ys)
-
-
-    def make_plot(self, plotwidget, style):
-        res = plotwidget.plot(self.xs, self.ys, name=self.name, **style)
-
-        if self.title:
-            plotwidget.setTitle(self.title)
-
-        if self.xlabel:
-            plotwidget.setLabel("bottom", self.xlabel)
-
-        if self.ylabel:
-            plotwidget.setLabel("left", self.ylabel)
-
-        return res
-
-
-

grum/exampledata.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from .descs import PlotDescription, ImageDescription
+from .plotdesc import PlotDescription
 
 
 X = np.arange(100) / 10
@@ -31,20 +31,4 @@ for name, (xs, ys) in exampledata_raw.items():
     )
 
 
-name = "image"
-xdim = ydim = 100
-size = xdim * ydim
-shape = (xdim, ydim)
-
-img = np.arange(size).reshape(shape) / size
-img += np.random.random(shape) / 10
-
-exampledata[name] = ImageDescription(
-    name,
-    image=img,
-    xlabel="x",
-    ylabel="y"
-)
-
-
 

grum/imgdesc.py

@@ -1,18 +1,19 @@
 import numpy as np
 import pyqtgraph as pg
-from .desc import Description
+
+from .theme import pg_legend_style
 
 
-class ImageDescription(Description):
+class ImageDescription:
 
-    def __init__(self, name, title=None, xlabel=None, ylabel=None, image=None, levels=None, cmap="viridis"):
+    def __init__(self, name, title=None, xlabel=None, ylabel=None, image=None, colormap=None, levels=None):
         self.name = name
         self.title = title
         self.xlabel = xlabel
         self.ylabel = ylabel
         self.image = image
-        self.levels = levels #TODO: might be better to use vmin and vmax
-        self.cmap = cmap
+        self.colormap = colormap
+        self.levels = levels
 
     @property
     def data(self):
@@ -22,7 +23,6 @@ class ImageDescription(Description):
     def data(self, value):
         self.image = value
 
-
     def append(self, xy):
         print("ignored image append")
 
@@ -31,22 +31,30 @@ class ImageDescription(Description):
 
 
     def make_plot(self, plotwidget, style):
-        res = plotwidget.setImage(self.data, levels=self.levels)
+        if self.levels:
+            res = plotwidget.setImage(self.data, levels = self.levels) #Set levels for histogram
+        else:
+            res = plotwidget.setImage(self.data)    
 
         if self.title:
             plotwidget.setTitle(self.title)
 
         if self.xlabel:
-            plotwidget.getView().setLabel("bottom", self.xlabel)
+            vbox = plotwidget.getView()
+            vbox.addItem(pg.LabelItem(self.xlabel, size='50pt'))
 
         if self.ylabel:
-            plotwidget.getView().setLabel("left", self.ylabel)
+            plotwidget.setLabel("left", self.ylabel)
 
-        if self.cmap:
-            cm = pg.colormap.get(self.cmap)
+        if self.colormap:
+            cm = pg.colormap.get(self.colormap)
             plotwidget.setColorMap(cm)
 
         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}
+
+
 

grum/mainwin.py

@@ -1,28 +1,26 @@
 from PyQt5.QtCore import Qt, pyqtSignal
 from PyQt5.QtWidgets import QMainWindow, QSplitter
+import pyqtgraph as pg
 
 from . import assets
-from .descs import DESC_TYPES, Description, ImageDescription, PlotDescription
 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
 from .rpc import RPCServerThread
 from .shortcut import shortcut
-from .webview import WebView
-
-
-DESC_TYPE_TO_MDI_SUB_TYPE = {
-    ImageDescription: MDISubImage,
-    PlotDescription:  MDISubPlot
-}
+# from .webview import WebView # doesnt work for CSAXS version of pyqtWebEngine
 
 
 class MainWindow(QMainWindow):
 
-    sig_make_new_subwin  = pyqtSignal(str, Description)
+    sig_make_new_plot = pyqtSignal(str, PlotDescription)
+    sig_make_new_image = pyqtSignal(str, ImageDescription)
 
     def __init__(self, *args, title="grum", host="localhost", port=8000, offline=False, add_examples=False, window_mode=MDIWindowMode.MULTI, **kwargs):
         super().__init__(*args, **kwargs)
@@ -34,7 +32,7 @@ class MainWindow(QMainWindow):
         self.setWindowIcon(assets.icon())
 
         url = f"http://{host}:{port}/"
-        self.webdoc = WebView(url, title=title)
+        # self.webdoc = WebView(url, title=title)  # doesnt work for CSAXS version of pyqtWebEngine
 
         self.lst = lst = DictList()
         lst.setAlternatingRowColors(True)
@@ -47,16 +45,21 @@ class MainWindow(QMainWindow):
         lst_menu.addSeparator()
         lst_menu.addAction("Plot selected", self.on_plot_selected)
         lst_menu.addSeparator()
-        lst_menu.addAction("Mark selected as seen", self.on_mark_selected_as_seen)
-        lst_menu.addAction("Mark selected as not seen", self.on_mark_selected_as_not_seen)
+        lst_menu.addAction("Mark selected as seen",
+                           self.on_mark_selected_as_seen)
+        lst_menu.addAction("Mark selected as not seen",
+                           self.on_mark_selected_as_not_seen)
         lst_menu.addSeparator()
         sort_group = lst_menu.addGroup()
-        sort_group.addCheckbox("Sort by insertion order", triggered=self.on_sort_by_insertion_order, state=True)
+        sort_group.addCheckbox(
+            "Sort by insertion order", triggered=self.on_sort_by_insertion_order, state=True)
         sort_group.addCheckbox("Sort by name", triggered=self.on_sort_by_name)
-        sort_group.addCheckbox("Sort by timestamp", triggered=self.on_sort_by_timestamp)
-        sort_group.addCheckbox("Sorting disabled", triggered=self.on_sorting_disabled)
+        sort_group.addCheckbox("Sort by timestamp",
+                               triggered=self.on_sort_by_timestamp)
+        sort_group.addCheckbox(
+            "Sorting disabled", triggered=self.on_sorting_disabled)
 
-        #TODO: clean up
+        # TODO: clean up
         def on_item_about_to_be_moved():
             sort_group.checkboxes["Sorting disabled"].setChecked(True)
             self.on_sorting_disabled()
@@ -76,7 +79,8 @@ class MainWindow(QMainWindow):
         self.menu_settings = menu = BarMenu(bar, "&Settings")
         menu.addCheckbox("Open new plots", state=True)
         menu.addSeparator()
-        menu.addEntrybox("Limit number of entries", placeholder="Maximum number of entries", triggered=lst.set_nkeep)
+        menu.addEntrybox("Limit number of entries",
+                         placeholder="Maximum number of entries", triggered=lst.set_nkeep)
 
         self.mdi = mdi = MDIArea(bar, window_mode=window_mode)
 
@@ -88,48 +92,40 @@ class MainWindow(QMainWindow):
         self.setCentralWidget(splitter)
 
         if not offline:
-            self.rst = rst = RPCServerThread(host, port, doc_title_suffix=title)
+            self.rst = rst = RPCServerThread(
+                host, port, doc_title_suffix=title)
             rst.start()
-            rst.server.register_function(self.new_image)
             rst.server.register_function(self.new_plot)
             rst.server.register_function(self.append_data)
             rst.server.register_function(self.extend_data)
             rst.server.register_function(self.set_data)
+            rst.server.register_function(self.new_image)
+            # function for CSAXS beamtime
+            rst.server.register_function(self.append_image_to_list)
+            # new function to get list of names from current grum session
+            rst.server.register_function(self.get_list_names)
+            # rst.server.register_function(self.plot_multiple_plots)
 
-        self.sig_make_new_subwin.connect(self.on_make_new_subwin)
-
+        self.sig_make_new_plot.connect(self.on_make_new_plot)
+        self.sig_make_new_image.connect(self.on_make_new_image)
 
     def keyPressEvent(self, event):
         if event.key() == Qt.Key_F1:
-            self.webdoc.show()
-
+            # self.webdoc.show() # doesnt work for CSAXS version of pyqtWebEngine
+            pass
 
     # Remote API calls
 
-    def new_image(self, name, cfg):
-        """
-        Create a new image <name> using the configuration dict <cfg>.
-        The configuration is forwarded to the constructor of ImageDescription.
-        Allowed keys are: title, xlabel, ylabel, image, levels, cmap.
-        """
-        desc = self.add_new_desc_to_list(ImageDescription, name, cfg)
-        if self.menu_settings.checkboxes["Open new plots"].isChecked():
-            sub = self.mdi.findSubWindow(name)
-            if sub:
-                sub.pw.setImage(desc.data) #TODO lacks the list sync
-            else:
-                self.sig_make_new_subwin.emit(name, desc)
-
     def new_plot(self, name, cfg):
         """
         Create a new plot <name> using the configuration dict <cfg>.
         The configuration is forwarded to the constructor of PlotDescription.
         Allowed keys are: title, xlabel, ylabel, xs, ys.
         """
-        desc = self.add_new_desc_to_list(PlotDescription, name, cfg)
+        desc = self.add_new_desc_to_list(name, cfg)
         if self.menu_settings.checkboxes["Open new plots"].isChecked():
             if not self.mdi.findSubWindow(name):
-                self.sig_make_new_subwin.emit(name, desc)
+                self.sig_make_new_plot.emit(name, desc)
 
     def append_data(self, name, point):
         """
@@ -161,13 +157,72 @@ class MainWindow(QMainWindow):
         desc.data = data
         self.sync_item_and_plots(item)
 
+    def new_image(self, name, cfg):
+        """
+        Create a new image <name> using the configuration dict <cfg>.
+        The configuration is forwarded to the constructor of ImageDescription.
+        Allowed keys are: title, xlabel, ylabel, image.
+        """
+        desc = self.add_new_desc_to_list(
+            name, cfg, Desc=ImageDescription)  # TODO: clean up Desc argument
+        if self.menu_settings.checkboxes["Open new plots"].isChecked():
+            sub = self.mdi.findSubWindow(name)
+            if sub:
+                sub.pw.setImage(desc.data)  # TODO lacks the list sync
+                vbox = sub.pw.getView()
+                allchildren = vbox.allChildren()
+                for child in allchildren:
+                    if isinstance(child, pg.LabelItem):
+                        vbox.removeItem(child)
+                vbox.addItem(pg.LabelItem(desc.xlabel, size='50pt'))
+
+            else:
+                self.sig_make_new_image.emit(name, desc)
+
+    def append_image_to_list(self, img):
+        desc = self.add_new_desc_to_list(img[0], img[1], Desc=ImageDescription)
+
+    def get_list_names(self):
+        return [key for key in self.lst.lst.items.keys()]
+
+    # def plot_multiple_plots(self, aa):
+
+    #     name = "plot 1"
+    #     cfg = {"xs": [0, 1], "ys": [3, 7]}
+    #     desc = self.add_new_desc_to_list(name, cfg)
+    #     name = "plot 2"
+    #     cfg = {"xs": [0, 3], "ys": [2,0]}
+    #     desc2 = self.add_new_desc_to_list(name, cfg)
+    #     items = [self.lst.get("plot 1"), self.lst.get("plot 2")]
+    #     self.plot_multiple_items(items)
+
+
+        # descs = {i.name: i for i in items}
+        # names = descs.keys()
+        # name = " | ".join(names)
+
+        # self.activate_or_make_subwin(MDISubMultiPlot, name, descs)
+
+        # if self.menu_settings.checkboxes["Open new plots"].isChecked():
+        #     if not self.mdi.findSubWindow(name):
+        #         self.sig_make_new_plot.emit(name, desc)
+
+        # self.make_subwin(MDISubMultiPlot, name, **descs)
+        # if not self.mdi.findSubWindow(name):
+        #     sub = MDISubMultiPlot(name, descs)
+        #     print("multi name", name)
+        #     print("multi descs", descs, *descs)
+        #     print("MULTI sub", sub)
+        #     print("multi mdi", self.mdi)
+        #     self.mdi.add(sub)
 
     # Signal callbacks
 
-    def on_make_new_subwin(self, name, desc):
-        DescType = type(desc)
-        MDISubType = DESC_TYPE_TO_MDI_SUB_TYPE[DescType]
-        self.make_subwin(MDISubType, name, desc)
+    def on_make_new_plot(self, *args, **kwargs):
+        self.make_subwin(MDISubPlot, *args, **kwargs)
+
+    def on_make_new_image(self, *args, **kwargs):
+        self.make_subwin(MDISubImage, *args, **kwargs)
 
     def on_dclick_list_item(self, item):
         self.plot_single_item(item)
@@ -179,17 +234,18 @@ class MainWindow(QMainWindow):
         if len(selected) == 1:
             item = selected[0]
             self.plot_single_item(item)
+        # TODO: what should be the typecheck?
+        elif type(selected[0].value) == ImageDescription:
+            self.plot_multiple_images(selected)
         else:
             self.plot_multiple_items(selected)
 
-
     def on_mark_selected_as_seen(self):
         self.lst.set_alarm_for_selected(False)
 
     def on_mark_selected_as_not_seen(self):
         self.lst.set_alarm_for_selected(True)
 
-
     def on_sort_by_insertion_order(self):
         self.lst.enable_sort_by_insertion_order()
 
@@ -202,7 +258,6 @@ class MainWindow(QMainWindow):
     def on_sorting_disabled(self):
         self.lst.disable_sorting()
 
-
     def on_file_open(self):
         fns = open_h5_files_dialog(self)
         if not fns:
@@ -210,11 +265,9 @@ class MainWindow(QMainWindow):
 
         for fn in fns:
             data = read_dict(fn)
-            for name, cfg in data.items():
-                tn = cfg.pop("type")
-                DescType = DESC_TYPES[tn]
-                self.add_new_desc_to_list(DescType, name, cfg)
-
+            for k, v in data.items():
+                Desc = ImageDescription if "image" in v else PlotDescription  # TODO
+                self.add_new_desc_to_list(k, v, Desc=Desc)
 
     def on_file_save(self):
         fn = save_h5_file_dialog(self)
@@ -228,11 +281,10 @@ class MainWindow(QMainWindow):
 
         write_dict(fn, data)
 
-
     # Plumbing
 
-    def add_new_desc_to_list(self, DescType, name, cfg):
-        desc = DescType(name, **cfg)
+    def add_new_desc_to_list(self, name, cfg, Desc=PlotDescription):  # TODO
+        desc = Desc(name, **cfg)
         self.lst.set(name, desc)
         return desc
 
@@ -251,26 +303,33 @@ class MainWindow(QMainWindow):
         item.timestamps.access.update()
         item.set_alarm(False)
         name, desc = item.key, item.value
-        DescType = type(desc)
-        MDISubType = DESC_TYPE_TO_MDI_SUB_TYPE[DescType]
+        MDISubType = MDISubImage if isinstance(
+            desc, ImageDescription) else MDISubPlot  # TODO
         self.activate_or_make_subwin(MDISubType, name, desc)
 
     def plot_multiple_items(self, items):
         for i in items:
             i.timestamps.access.update()
             i.set_alarm(False)
-        items = (i for i in items if isinstance(i.value, PlotDescription)) #TODO: for now, only overlay plots
         descs = {i.key: i.value for i in items}
         names = descs.keys()
         name = " | ".join(names)
         self.activate_or_make_subwin(MDISubMultiPlot, name, descs)
 
+    def plot_multiple_images(self, 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)
+        self.activate_or_make_subwin(MDISubMultiImage, name, descs)
 
-    #TODO: the following two could be methods of MDIArea?
+    # TODO: the following two could be methods to MDIArea?
 
     def activate_or_make_subwin(self, MDISubType, name, *args, **kwargs):
         sub = self.mdi.findSubWindow(name)
-        if sub: #TODO check type? what to do for mismatches?
+        if sub:  # TODO check type? what to do for mismatches?
             self.mdi.setActiveSubWindow(sub)
         else:
             self.make_subwin(MDISubType, name, *args, **kwargs)
@@ -278,6 +337,3 @@ class MainWindow(QMainWindow):
     def make_subwin(self, MDISubType, name, *args, **kwargs):
         sub = MDISubType(name, *args, **kwargs)
         self.mdi.add(sub)
-
-
-

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

@@ -1,26 +1,33 @@
 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(view=pg.PlotItem()) # for axis ticks and labels, view needs to be a PlotItem
+        
+        self.pw = pw = pg.ImageView()
         self.setWidget(pw)
 
         # connect to plot mouse-over event
         pw.scene.sigMouseMoved.connect(self.on_hover)
 
         style = pg_plot_style()
+        # cm = pg.colormap.get('CET-C1')
+        # pw.setColorMap(cm)
 
         plot = desc.make_plot(self.pw, style)
         self.plots = {name: plot}
-
         self.image = desc.data
 
-
     def on_hover(self, event):
         coord = self.pw.imageItem.mapFromScene(event)
         x = coord.x()
@@ -35,4 +42,56 @@ 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.pw = pw = pg.ImageView()
+
+        self.central_widget = QWidget()
+        self.button_next = QPushButton('Next', self.central_widget)
+        self.button_previous = QPushButton('Previous', self.central_widget)
+        self.slider = QSlider(Qt.Horizontal)
+        self.slider.setRange(0,len(descs)-1)
+
+        self._create_layout()
+        self._connect_signals()
+
+        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
+
+    def _create_layout(self):
+        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)
+
+    def _connect_signals(self):
+        self.button_next.clicked.connect(lambda:self.update_slider(1))
+        self.button_previous.clicked.connect(lambda:self.update_slider(-1))
+        self.slider.valueChanged.connect(self.update_img)
+        
+    def update_slider(self, value):
+        self.slider.setValue(self.slider.value()+value)
+
+    def update_img(self, value):
+        self.pw.setImage(self.descriptions[value].data)
+        self.set_title_in_image()
+
+    def set_title_in_image(self):
+        if self.descriptions[self.slider.value()].xlabel:
+            vbox = self.pw.getView()
+            allchildren = vbox.allChildren()
+            for child in allchildren: 
+                if isinstance(child, pg.LabelItem):
+                    vbox.removeItem(child)
+            vbox.addItem(pg.LabelItem(self.descriptions[self.slider.value()].xlabel, size='50pt'))

grum/mdi/mdisubwin.py

@@ -4,17 +4,12 @@ from PyQt5.QtWidgets import QMdiSubWindow
 from .. import assets
 
 
-SUB_WIN_WIDTH  = 640
-SUB_WIN_HEIGHT = 480
-
-
 class MDISubWindow(QMdiSubWindow):
 
     def __init__(self, title, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.setWindowTitle(title)
         self.setWindowIcon(assets.char())
-        self.resize(SUB_WIN_WIDTH, SUB_WIN_HEIGHT)
 
         # without this, the SubWindow is not removed from the subWindowList
         self.setAttribute(Qt.WA_DeleteOnClose)

grum/plot_multiple_phases.py

@@ -0,0 +1,78 @@
+from grum.rpc import RPCClient
+from os import listdir
+from os.path import isfile, join
+import h5py
+import numpy as np
+import argparse
+
+class plotPhases:
+    """
+    A possibility to plot reconstructions in a scan number range
+    """
+    def __init__(self, start, end, step=1):
+        self.start = start
+        self.end = end
+        self.step =step
+        self.eaccount = "e20631"
+        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)
+            print("appending scan nr: ", scan_nr)
+            self.grum_client.append_image_to_list([f"{scan_nr} Phase", {'image': recon_img_phase, "xlabel": xlab}])
+            # self.image_description_list.append([f"{scan_nr} Phase", {'image': recon_img_phase, "xlabel": xlab}])
+
+        # print("calling plot images from list")
+        # self.grum_client.append_images_to_list(self.image_description_list)        
+
+    def get_recon_phase(self, hf):
+    
+        recon_object = hf.get('reconstruction/object')
+
+        recon_object = np.array(recon_object)
+        recon_object_angle = np.angle(recon_object)
+        
+        recon_object_angle = np.rot90(recon_object_angle, 3)
+        recon_img_angle = recon_object_angle.tolist()
+        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 for 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 = 5037 # default
+    end = 5038 # default
+    step = 1
+    
+    parser = argparse.ArgumentParser(description="description", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("-s", "--startend", nargs =2, help="set start, end")
+    clargs = parser.parse_args()
+    if clargs:
+        start = int(clargs.startend[0])
+        end = int(clargs.startend[1])
+    
+    print('starts plotting phase for scans: ',start, ' to ', end)
+    pp = plotPhases(start, end)
+    pp.plot_all_phases()

grum/plotdesc.py

@@ -0,0 +1,66 @@
+from pyqtgraph import DateAxisItem
+from collections import deque
+
+class PlotDescription:
+
+    def __init__(self, name, title=None, xlabel=None, ylabel=None, xs=None, ys=None, frmt=None, time=False):
+        self.name = name
+        self.title = title
+        self.xlabel = xlabel
+        self.ylabel = ylabel
+        self.xs = deque(maxlen = 5000) if xs is None else deque(xs, maxlen = 5000)
+        self.ys = deque(maxlen = 5000) if ys is None else deque(ys, maxlen = 5000) 
+        self.format = frmt
+        self.time = time
+
+    @property
+    def data(self):
+        return (self.xs, self.ys)
+
+    @data.setter
+    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 extend(self, data):
+        xs, ys = data
+        self.xs.extend(xs)
+        self.ys.extend(ys)
+
+    def make_plot(self, plotwidget, style):
+        if self.format:
+            res = self.plot_with_format(plotwidget, style)
+        else:
+            res = plotwidget.plot(self.xs, self.ys, name=self.name, **style)
+        
+        if self.time:
+            axis = DateAxisItem()
+            plotwidget.setAxisItems({'bottom':axis})
+
+        if self.title:
+            plotwidget.setTitle(self.title)
+
+        if self.xlabel:
+            plotwidget.setLabel("bottom", self.xlabel)
+
+        if self.ylabel:
+            plotwidget.setLabel("left", self.ylabel)
+
+        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(self, plotwidget, style):
+        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)

grum/webview.py

@@ -2,7 +2,7 @@ from PyQt5.QtCore import QUrl
 
 try:
     from PyQt5.QtWebKitWidgets import QWebView
-except (ImportError, ModuleNotFoundError):
+except ImportError:
     from PyQt5.QtWebEngineWidgets import QWebEngineView as QWebView
 
 

setup.cfg

@@ -4,9 +4,9 @@ version = 0.0.1
 description = GUI for Remote Unified Monitoring
 long_description = file: README.md
 long_description_content_type = text/markdown
-url = https://gitea.psi.ch/SwissFEL/grum
+url = https://gitlab.psi.ch/augustin_s/grum
 project_urls =
-    Bug Tracker = https://gitea.psi.ch/SwissFEL/grum/issues
+    Bug Tracker = https://gitlab.psi.ch/augustin_s/grum/issues
 classifiers =
     Programming Language :: Python :: 3
     License :: OSI Approved :: MIT License

setup.py

@@ -1,8 +1,18 @@
+import os
+import pathlib
+import subprocess
+
 from setuptools import setup
 
+CURRENT_PATH = pathlib.Path(__file__).parent.resolve()
+
+# bec_utils = os.path.join(os.getenv("BEC_PATH", f"{CURRENT_PATH}/../bec"), "bec_utils")
+
 if __name__ == "__main__":
+    # subprocess.run(f"pip install -e {bec_utils}", shell=True, check=True)
+
     setup(
-        install_requires=["pyqt5", "pyqtgraph", "h5py", "PyQtWebEngine"],
+        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"]},
     )
 

tests/test_mainwin.py

@@ -14,7 +14,7 @@ from grum.mainwin import MainWindow
 from grum.mdi import MDIArea, MDISubMultiPlot, MDISubPlot
 from grum.menus import BarMenu
 from grum.menus.rclickmenu import RClickMenu
-from grum.descs import Description, PlotDescription
+from grum.plotdesc import PlotDescription
 from grum.rpc import RPCServerThread
 
 
@@ -47,7 +47,7 @@ class TestMainWin:
 
         for key in mw.lst.lst.items:
             assert isinstance(mw.lst.lst.get(key), DictListItem)
-            assert isinstance(mw.lst.lst.get(key).value, Description)
+            assert isinstance(mw.lst.lst.get(key).value, PlotDescription)
 
         assert isinstance(mw.lst.menu, RClickMenu)
         assert isinstance(mw.menu_settings, BarMenu)
@@ -65,7 +65,7 @@ class TestMainWin:
         xlabel = "xlabel"
         ylabel = "ylabel"
         cfg = {"title": title, "xlabel": xlabel, "ylabel": ylabel}
-        spy_sig_make_new_subwin = QSignalSpy(mw.sig_make_new_subwin)
+        spy_sig_make_new_plot = QSignalSpy(mw.sig_make_new_plot)
 
         mw.new_plot(name, cfg=cfg)
 
@@ -76,28 +76,28 @@ class TestMainWin:
         assert mw.lst.lst.get(name).value.ylabel == ylabel
 
         assert mw.menu_settings.checkboxes["Open new plots"].isChecked()
-        assert len(spy_sig_make_new_subwin) == 1  # assert called once
-        assert spy_sig_make_new_subwin[0][0] == name  # assert called with name
-        assert isinstance(spy_sig_make_new_subwin[0][1], PlotDescription)
+        assert len(spy_sig_make_new_plot) == 1  # assert called once
+        assert spy_sig_make_new_plot[0][0] == name  # assert called with name
+        assert isinstance(spy_sig_make_new_plot[0][1], PlotDescription)
 
         mw.menu_settings.checkboxes["Open new plots"].setChecked(False)
         assert mw.menu_settings.checkboxes["Open new plots"].isChecked() == False
-        spy_sig_make_new_subwin = QSignalSpy(mw.sig_make_new_subwin)
+        spy_sig_make_new_plot = QSignalSpy(mw.sig_make_new_plot)
 
         mw.new_plot("new_name", cfg)
 
-        assert len(spy_sig_make_new_subwin) == 0  # assert not called
+        assert len(spy_sig_make_new_plot) == 0  # assert not called
 
         mw.menu_settings.checkboxes["Open new plots"].setChecked(True)
         assert mw.menu_settings.checkboxes["Open new plots"].isChecked() == True
-        spy_sig_make_new_subwin = QSignalSpy(mw.sig_make_new_subwin)
+        spy_sig_make_new_plot = QSignalSpy(mw.sig_make_new_plot)
         new_name_item = mw.lst.lst.get("new_name")
         sub = MDISubPlot("new_name", new_name_item.value)
         mw.mdi.add(sub)
 
         mw.new_plot("new_name", cfg)
 
-        assert len(spy_sig_make_new_subwin) == 0  # assert not called
+        assert len(spy_sig_make_new_plot) == 0  # assert not called
 
 
     def test_append_data(self):
@@ -122,19 +122,17 @@ class TestMainWin:
         assert sine_item.set_alarm.call_args[0][0] == False
 
 
-    def test_on_make_new_subwin(self):
+    def test_on_make_new_plot(self):
         mw = self.mw
 
         mw.make_subwin = mock.MagicMock()
 
-        name = "test"
-        cfg = {"title": "title"}
+        args = (1, 2, "name")
+        kwargs = {"title": "plot_title"}
 
-        desc = PlotDescription(name, *cfg)
+        mw.on_make_new_plot(args, kwargs)
 
-        mw.on_make_new_subwin(name, desc)
-
-        mw.make_subwin.assert_called_once_with(MDISubPlot, name, desc)
+        mw.make_subwin.assert_called_once_with(MDISubPlot, args, kwargs)
 
 
     def test_on_dclick_list_item(self):

tests/test_plotdesc.py

@@ -6,7 +6,7 @@ import pyqtgraph as pg
 from grum import theme
 from grum.mainwin import MainWindow
 from grum.mdi.mdisubplot import MDISubPlot
-from grum.descs import PlotDescription
+from grum.plotdesc import PlotDescription
 from grum.theme import pg_plot_style
 
 
@@ -78,7 +78,6 @@ def test_to_dict():
         "xs": [1, 2],
         "ylabel": "plot_ylabel",
         "ys": [3, 4],
-        "type": "plot"
     }