Merge pull request #321 from dmgav/lazy-loading

'Lazy' loading of Dask arrays from Tiled (SRX)

pyxrf/model/lineplot.py

@@ -10,7 +10,7 @@
 import numpy as np
 from atom.api import Atom, Bool, Dict, Float, Int, List, Str, Typed, observe
 from matplotlib.axes import Axes
-from matplotlib.collections import BrokenBarHCollection
+from matplotlib.collections import PolyCollection
 from matplotlib.colors import LogNorm
 from matplotlib.figure import Figure
 from matplotlib.lines import Line2D
@@ -122,7 +122,7 @@ class LinePlotModel(Atom):
     _fig_preview = Typed(Figure)
     _ax_preview = Typed(Axes)
     _lines_preview = List()
-    _bahr_preview = Typed(BrokenBarHCollection)
+    _bahr_preview = Typed(PolyCollection)
 
     plot_type_preview = Typed(PlotTypes)
     energy_range_preview = Typed(EnergyRangePresets)
@@ -177,7 +177,7 @@ class LinePlotModel(Atom):
     show_exp_opt = Bool(False)  # Flag: show spectrum preview
 
     # Reference to artist responsible for displaying the selected range of energies on the plot
-    plot_energy_barh = Typed(BrokenBarHCollection)
+    plot_energy_barh = Typed(PolyCollection)
     t_bar = Typed(object)
 
     plot_exp_list = List()
@@ -727,7 +727,7 @@ def plot_selected_energy_range_original(self, *, e_low=None, e_high=None):
             self.plot_energy_barh.remove()
 
         # Create the new plot (based on new parameters if necessary
-        self.plot_energy_barh = BrokenBarHCollection.span_where(
+        self.plot_energy_barh = PolyCollection.span_where(
             x_v, ymin=y_min, ymax=y_max, where=ss, facecolor="white", edgecolor="yellow", alpha=1
         )
         self._ax.add_collection(self.plot_energy_barh)
@@ -1471,7 +1471,7 @@ def plot_selected_energy_range(self, *, axes, barh_existing, e_low=None, e_high=
             barh_existing.remove()
 
         # Create the new plot (based on new parameters if necessary
-        barh_new = BrokenBarHCollection.span_where(
+        barh_new = PolyCollection.span_where(
             x_v, ymin=y_min, ymax=y_max, where=ss, facecolor="white", edgecolor="yellow", alpha=1
         )
         axes.add_collection(barh_new)

pyxrf/model/load_data_from_db.py

@@ -2318,20 +2318,24 @@ def map_data2D_srx_new_tiled(
 
         d_xs, d_xs_sum, N_xs, d_xs2, d_xs2_sum, N_xs2 = None, None, 0, None, None, 0
         if "xs_fluor" in data_stream0:
-            d_xs = data_stream0["xs_fluor"]
+            # The type of loaded data is tiled.client.array.DaskArrayClient
+            #   If the data is not explicitly converted to da.array, then da.sum
+            #   will fill the whole dataset, which is not desirable. This could be
+            #   fixed in the future versions of Tiled.
+            d_xs = da.array(data_stream0["xs_fluor"])
             d_xs_sum = da.sum(d_xs, 2)
             N_xs = d_xs.shape[2]
         elif "fluor" in data_stream0:  # Old format
-            d_xs = data_stream0["fluor"]
+            d_xs = da.array(data_stream0["fluor"])
             d_xs_sum = da.sum(d_xs, 2)
             N_xs = d_xs.shape[2]
 
         if "xs_fluor_xs2" in data_stream0:
-            d_xs2 = data_stream0["xs_fluor_xs2"]
+            d_xs2 = da.array(data_stream0["xs_fluor_xs2"])
             d_xs2_sum = da.sum(d_xs2, 2)
             N_xs2 = d_xs2.shape[2]
         elif "fluor_xs2" in data_stream0:  # Old format
-            d_xs2 = data_stream0["fluor_xs2"]
+            d_xs2 = da.array(data_stream0["fluor_xs2"])
             d_xs2_sum = da.sum(d_xs2, 2)
             N_xs2 = d_xs2.shape[2]
 
@@ -2536,10 +2540,12 @@ def swap_axes():
 
         # Replace NaNs with 0s (in corrupt data rows).
         loaded_data = {}
-        loaded_data["det_sum"] = np.nan_to_num(tmp_data_sum.compute())
+        # loaded_data["det_sum"] = np.nan_to_num(tmp_data_sum.compute())
+        loaded_data["det_sum"] = tmp_data_sum
         if create_each_det:
             for i in range(num_det):
-                loaded_data["det" + str(i + 1)] = np.nan_to_num(da.squeeze(tmp_data[:, :, i, :]).compute())
+                # loaded_data["det" + str(i + 1)] = np.nan_to_num(da.squeeze(tmp_data[:, :, i, :]).compute())
+                loaded_data["det" + str(i + 1)] = da.squeeze(tmp_data[:, :, i, :])
 
         if save_scaler:
             loaded_data["scaler_data"] = sclr.compute()
@@ -3519,6 +3525,8 @@ def save_data_to_hdf5(
         Failed to write data to HDF5 file.
     """
 
+    time_start = ttime.time()
+
     fpath = os.path.expanduser(fpath)
     fpath = os.path.abspath(fpath)
 
@@ -3539,22 +3547,23 @@ def incorrect_type_msg(channel, data_type):
             f"The data is converted from '{data_type}' to 'np.float32' before saving to file."
         )
 
-    if "det_sum" in data and isinstance(data["det_sum"], np.ndarray):
+    if "det_sum" in data and isinstance(data["det_sum"], (np.ndarray, da.core.Array)):
         if data["det_sum"].dtype != np.float32:
             incorrect_type_msg("det_sum", data["det_sum"].dtype)
             data["det_sum"] = data["det_sum"].astype(np.float32, copy=False)
         sum_data = data["det_sum"]
         sum_data_exists = True
 
     for detname in xrf_det_list:
-        if detname in data and isinstance(data[detname], np.ndarray):
+        if detname in data and isinstance(data[detname], (np.ndarray, da.core.Array)):
             if data[detname].dtype != np.float32:
                 incorrect_type_msg(detname, data[detname].dtype)
                 data[detname] = data[detname].astype(np.float32, copy=False)
 
             if not sum_data_exists:  # Don't compute it if it already exists
                 if sum_data is None:
-                    sum_data = np.copy(data[detname])
+                    # sum_data = np.copy(data[detname])
+                    sum_data = data[detname].copy()
                 else:
                     sum_data += data[detname]
 
@@ -3598,18 +3607,59 @@ def incorrect_type_msg(channel, data_type):
             for key, value in metadata_prepared.items():
                 metadata_grp.attrs[key] = value
 
+        # The following parameters control how data is loaded from Tiled
+        n_pixels_in_batch = 40000
+        n_tiled_download_retries = 10
+
+        def compute_batch_params(shape):
+            n_rows, n_cols = shape[0], shape[1]
+            n_rows_batch = max(int(n_pixels_in_batch / n_cols), 1)  # Save at least one row
+            n_batches = int(n_rows / n_rows_batch)
+            if n_rows % n_rows_batch:
+                n_batches += 1
+            return n_rows, n_rows_batch, n_batches
+
+        def download_dataset(dset, data):
+            n_rows, n_rows_batch, n_batches = compute_batch_params(sum_data.shape)
+            for n in range(n_batches):
+                ns, ne = n * n_rows_batch, min((n + 1) * n_rows_batch, n_rows)
+                for retry in range(n_tiled_download_retries):
+                    try:
+                        dset[ns:ne, ...] = np.nan_to_num(np.array(data[ns:ne, ...]))
+                        break
+                    except Exception as ex:
+                        logger.error(f"Failed to load the batch: {ex}")
+                    if retry >= n_tiled_download_retries - 1:
+                        raise TimeoutError("Failed to download data from Tiled server")
+                print(f"  Number of saved rows: {ne}")
+
         if create_each_det is True:
             for detname in xrf_det_list:
-                new_data = data[detname]
-                dataGrp = f.create_group(interpath + "/" + detname)
-                ds_data = dataGrp.create_dataset("counts", data=new_data, compression="gzip")
-                ds_data.attrs["comments"] = "Experimental data from {}".format(detname)
+                if not isinstance(sum_data, da.core.Array):
+                    new_data = data[detname]
+                    dataGrp = f.create_group(interpath + "/" + detname)
+                    ds_data = dataGrp.create_dataset("counts", data=new_data, compression="gzip")
+                    ds_data.attrs["comments"] = "Experimental data from {}".format(detname)
+                else:
+                    new_data = data[detname]
+                    dataGrp = f.create_group(interpath + "/" + detname)
+                    ds_data = dataGrp.create_dataset("counts", new_data.shape, compression="gzip")
+                    print(f"Downloading data: channel {detname!r} ...")
+                    download_dataset(ds_data, new_data)
+                    ds_data.attrs["comments"] = "Experimental data from {}".format(detname)
 
         # summed data
         if sum_data is not None:
-            dataGrp = f.create_group(interpath + "/detsum")
-            ds_data = dataGrp.create_dataset("counts", data=sum_data, compression="gzip")
-            ds_data.attrs["comments"] = "Experimental data from channel sum"
+            if not isinstance(sum_data, da.core.Array):
+                dataGrp = f.create_group(interpath + "/detsum")
+                ds_data = dataGrp.create_dataset("counts", data=sum_data, compression="gzip")
+                ds_data.attrs["comments"] = "Experimental data from channel sum"
+            else:
+                dataGrp = f.create_group(interpath + "/detsum")
+                ds_data = dataGrp.create_dataset("counts", sum_data.shape, compression="gzip")
+                print("Downloading data: the sum of all channels ...")
+                download_dataset(ds_data, sum_data)
+                ds_data.attrs["comments"] = "Experimental data from channel sum"
 
         # add positions
         if "pos_names" in data:
@@ -3627,6 +3677,8 @@ def incorrect_type_msg(channel, data_type):
             dataGrp.create_dataset("name", data=helper_encode_list(scaler_names))
             dataGrp.create_dataset("val", data=scaler_data)
 
+        logger.info(f"Total data saving time: {ttime.time() - time_start}")
+
     return fpath