Merge pull request #122 from usnistgov/121-bug-sst1rsoxsdb-scan-hinti…

…ng-breaks-if-a-scanned-axis-has-negative-value

`SST1RSoXSDB`: fix bug described in  #121

src/PyHyperScattering/SST1RSoXSDB.py

@@ -66,6 +66,7 @@ def __init__(
         catalog_kwargs={},
         use_precise_positions=False,
         use_chunked_loading=False,
+        suppress_time_dimension=True,
     ):
         """
         Args:
@@ -77,6 +78,7 @@ def __init__(
             catalog_kwargs (dict): kwargs to be passed to a from_profile catalog generation script.  For example, you can ask for Dask arrays here.
             use_precise_positions (bool): if False, rounds sam_x and sam_y to 1 digit.  If True, keeps default rounding (4 digits).  Needed for spiral scans to work with readback positions.
             use_chunked_loading (bool): if True, returns Dask backed arrays for further Dask processing.  if false, behaves in conventional Numpy-backed way
+            suppress_time_dimension (bool): if True, time is never a dimension that you want in your data and will be dropped (default).  if False, time will be a dimension in almost every scan.
         """
 
         if corr_mode == None:
@@ -114,6 +116,7 @@ def __init__(
         self.dark_pedestal = dark_pedestal
         self.exposure_offset = exposure_offset
         self.use_precise_positions = use_precise_positions
+        self.suppress_time_dimension = suppress_time_dimension
 
     # def loadFileSeries(self,basepath):
     #     try:
@@ -287,7 +290,7 @@ def searchCatalog(
             # Skip arguments with value None, and quits if the catalog was reduced to 0 elements
             if (searchSeries[1] is not None) and (len(reducedCatalog) > 0):
                 # For numeric entries, do Key equality
-                if "numeric" in str(searchSeries[2]):
+                if "numeric" in str(searchSeries.iloc[2]):
                     reducedCatalog = reducedCatalog.search(
                         Key(searchSeries.iloc[0]) == float(searchSeries.iloc[1])
                     )
@@ -568,11 +571,11 @@ def loadRun(
             raw (xarray): raw xarray containing your scan in PyHyper-compliant format
 
         """
-        if type(run) is int:
+        if isinstance(run,int):
             run = self.c[run]
-        elif type(run) is pd.DataFrame:
+        elif isinstance(run,pd.DataFrame):
             run = list(run.scan_id)
-        if type(run) is list:
+        if isinstance(run,list):
             return self.loadSeries(
                 run,
                 "sample_name",
@@ -606,30 +609,39 @@ def loadRun(
             else:
                 axes_to_include = []
                 rsd_cutoff = 0.005
-
+            
                 # begin with a list of the things that are primary streams
                 axis_list = list(run["primary"]["data"].keys())
+
                 # next, knock out anything that has 'image', 'fullframe' in it - these aren't axes
                 axis_list = [x for x in axis_list if "image" not in x]
                 axis_list = [x for x in axis_list if "fullframe" not in x]
                 axis_list = [x for x in axis_list if "stats" not in x]
                 axis_list = [x for x in axis_list if "saturated" not in x]
                 axis_list = [x for x in axis_list if "under_exposed" not in x]
+
                 # knock out any known names of scalar counters
                 axis_list = [x for x in axis_list if "Beamstop" not in x]
                 axis_list = [x for x in axis_list if "Current" not in x]
 
+                if self.suppress_time_dimension:
+                    axis_list = [x for x in axis_list if x != "time"]
+
                 # now, clean up duplicates.
                 axis_list = [x for x in axis_list if "setpoint" not in x]
                 # now, figure out what's actually moving.  we use a relative standard deviation to do this.
                 # arbitrary cutoff of 0.5% motion = it moved intentionally.
                 for axis in axis_list:
                     std = np.std(run["primary"]["data"][axis])
-                    mean = np.mean(run["primary"]["data"][axis])
-                    rsd = std / mean
-
+                    motion = np.abs(np.max(run["primary"]["data"][axis])-np.min(run["primary"]["data"][axis]))
+                    if motion == 0:
+                        rsd = 0
+                    else:
+                        rsd = std / motion
+                    #print(f'Evaluating {axis} for inclusion as a dimension with rsd {rsd}...')
                     if rsd > rsd_cutoff:
                         axes_to_include.append(axis)
+                        #print(f'    --> it was included')
 
                 # next, construct the reverse lookup table - best mapping we can make of key to pyhyper word
                 # we start with the lookup table used by loadMd()
@@ -681,15 +693,11 @@ def loadRun(
         """
 
         data = run["primary"]["data"][md["detector"] + "_image"]
-        if (
-            type(data) == tiled.client.array.ArrayClient
-            or type(data) == tiled.client.array.DaskArrayClient
-        ):
+        if isinstance(data,tiled.client.array.ArrayClient):
+            data = run["primary"]["data"].read()[md["detector"] + "_image"]
+        elif isinstance(data,tiled.client.array.DaskArrayClient):
             data = run["primary"]["data"].read()[md["detector"] + "_image"]
-        elif type(data) == tiled.client.array.DaskArrayClient:
-            data = xr.DataArray(
-                data.read(), dims=data.dims
-            )  # xxx hack!  Really should use tiled structure_clients xarraydaskclient here.
+
         data = data.astype(int)  # convert from uint to handle dark subtraction
 
         if self.dark_subtract:
@@ -707,7 +715,7 @@ def loadRun(
             def subtract_dark(img, pedestal=100, darks=None):
                 return img + pedestal - darks[int(img.dark_id.values)]
 
-            data = data.groupby("time").map(subtract_dark, darks=dark, pedestal=self.dark_pedestal)
+            data = data.groupby("time",squeeze=False).map(subtract_dark, darks=dark, pedestal=self.dark_pedestal)
 
         dims_to_join = []
         dim_names_to_join = []
@@ -733,11 +741,12 @@ def subtract_dark(img, pedestal=100, darks=None):
         if len(index) != len(data["time"]):
             index = index[: len(data["time"])]
         actual_exposure = md["exposure"] * len(data.dim_0)
+        mindex_coords = xr.Coordinates.from_pandas_multiindex(index, 'system')
         retxr = (
             data.sum("dim_0")
             .rename({"dim_1": "pix_y", "dim_2": "pix_x"})
             .rename({"time": "system"})
-            .assign_coords(system=index)
+            .assign_coords(mindex_coords)
         )  # ,md['detector']+'_image':'intensity'})
 
         # this is needed for holoviews compatibility, hopefully does not break other features.
@@ -776,7 +785,7 @@ def subtract_dark(img, pedestal=100, darks=None):
             retxr = retxr / monitors["RSoXS Au Mesh Current"]
         elif self.corr_mode != "none":
             warnings.warn(
-                "corrections other than none are not supported at the moment",
+                "corrections other than none or i0 are not supported at the moment",
                 stacklevel=2,
             )