adding PLProcessing test data (#6)

* PLProcessing working

* datasets tweak

Author: ddkohler

examples/PLProcessing.py

@@ -1,27 +1,27 @@
 
 # Process PL Data from Wright group
 
-import pathlib
 import makeitwright as mw
-
+from makeitwright import datasets
 
 andor = mw.andor
 roi = mw.helpers.roi
 parse = mw.parsers.parse
 plot = mw.spectra.plot_spectra
 
+p = datasets.PL  
+filepath = p.parent
+filename = p.stem
 
-filepath = pathlib.Path().expanduser() / "Desktop" / "Research Data" / "Wright Table" / "Original" / "test"
-filename = "PEAPbI on FPEASnI PL 77K 4 2 hour wait for cool"
-obj = 10            # Objective magnification (5x, 10x, 50x, 100x)
-ROI_lower = 1000    # Lower and upper bounds of ROI
-ROI_upper = 1047
+obj = 10          # Objective magnification (5x, 10x, 50x, 100x)
+ROI_lower = 575    # Lower and upper bounds of ROI
+ROI_upper = 600
 plotx_lower = 500   # Lower and upper bounds of built-in plot x-axis
 plotx_upper = 800
 
 
 # Read data
-data = parse(filepath, objective=obj, keywords=filename + ".asc")
+data = parse(filepath, objective=str(obj), keywords=filename + ".asc")
 
 
 # Check object area
@@ -34,7 +34,6 @@
     if con == '1':
         quit()
 
-
 # Process PL data
 PL_ROI = roi(data, {'y': ([ROI_lower, ROI_upper], 'average')})
 plot(PL_ROI, channel=0, xrange=[plotx_lower, plotx_upper])      # Can add vrange=[ , ] (y axis scale)

makeitwright/core/parsers/__init__.py

@@ -11,6 +11,18 @@
 from .xrd import fromBruker
 
 
+px_per_um = {
+    '5x-Jin' : 0.893,
+    '20x-Jin' : 3.52, 
+    '100x-Wright' : 18.2,
+    '5' : 0.893,
+    '20' : 3.52,
+    '100' : 18.2,
+}
+# add 10x for now with approximation
+px_per_um["10"] = px_per_um["10x-Jin"] = 2 * px_per_um["5"]
+
+
 def typeID(*fpaths):
     """
     Infer what kind of data the file contains.
@@ -78,14 +90,14 @@ def parse(fdir, objective, select_types=None, keywords:list|str=[], exclude=[]):
             keywords = [keywords]
         for kw in keywords:
             for i, f in enumerate(files):
-                if kw not in f:
+                if kw not in str(f):
                     include[i]=0
     if exclude:
         if type(exclude) is not list:
             exclude = [exclude]
         for x in exclude:
             for i, f in enumerate(files):
-                if x in f:
+                if x in str(f):
                     include[i]=0
 
     files = [file for i, file in zip(include, files) if i]
@@ -118,15 +130,15 @@ def parse(fdir, objective, select_types=None, keywords:list|str=[], exclude=[]):
         too_much_data = True
     if len(ftypes) > 200:
         too_much_data = True
-    if sum([f.state()["st_size"] for f in files]) > virtual_memory().available:
+    if sum([f.stat().st_size for f in files]) > virtual_memory().available:
         too_much_data = True
 
     if too_much_data:
         raise MemoryError("too much data in directory, parsing cancelled to prevent storage overflow")
 
     d = []
     for fpath, dtype in ftypes.items():
-        basename = fpath.split('/')[-1].split('.')[0]
+        basename = fpath.stem
 
         if dtype.startswith('LabramHR'):
             d.append(fromLabramHR(fpath, name=basename))
@@ -148,9 +160,10 @@ def parse(fdir, objective, select_types=None, keywords:list|str=[], exclude=[]):
 
         elif dtype=='ASCII':
             try:
-                d.append(fromAndorNeo(fpath, name=basename, objective_lens=objective))
-            except:
+                d.append(fromAndorNeo(fpath, name=basename, px_per_um=px_per_um[objective] if objective else None))
+            except Exception as e:
                 print(f'attempted to extract ASCII data from path <{fpath}> but it was not recognized by the andor module')
+                raise e
             print(basename)
 
         elif dtype=='wt5':

makeitwright/core/parsers/andor.py

@@ -1,10 +1,11 @@
 import WrightTools as wt
-import numpy as np
-import pathlib
-from os import fspath
 
 
-def fromAndorNeo(fpath, name=None, objective_lens='prompt', cps=False):
+# builtin conversion from pixels to um (from somebody's records)
+# for different objectives
+# roughly, pixel size in microns / magnification
+
+def fromAndorNeo(fpath, name=None, px_per_um=None):
     """Create a data object from Andor Solis software (ascii exports).
 
     Parameters
@@ -16,169 +17,35 @@ def fromAndorNeo(fpath, name=None, objective_lens='prompt', cps=False):
     name : string (optional)
         Name to give to the created data object. If None, filename is used.
         Default is None.
+    px_per_um : float-like (optional)
+        if present, camera spatial dimensions will be mapped in micron units.
+        if not present, spatial variables of camera will be a unitless index
 
     Returns
     -------
     data
         New data object.
     """
-
-    objective_lenses = {
-        '5x-Jin' : 0.893,
-        '20x-Jin' : 3.52, 
-        '100x-Wright' : 18.2,
-        '5' : 0.893,
-        '20' : 3.52,
-        '100' : 18.2,
-        5 : 0.893,
-        20 : 3.52,
-        100 : 18.2
-    }
-
     # parse filepath
-    filepath = pathlib.Path(fpath)
-
-    if not ".asc" in filepath.suffixes:
-        wt.exceptions.WrongFileTypeWarning.warn(filepath, ".asc")
-    # parse name
-    if name is None:
-        name = filepath.name.split("/")[-1]
+    data:wt.Data = wt.data.from_Solis(fpath, name=name, verbose=True)
+    data.rename_variables(xindex="x", yindex="y", wm="wl")
+    data.rename_channels(signal="sig")
 
-    if objective_lens=='prompt':
-        objective_lens = input(f'enter magnification for data at {name}: ')
-        if not objective_lens:
-            objective_lens = 0
+    for var in {"x", "y"} & set(data.variable_names):
+        if px_per_um:
+            data[var][:] = data[var][:] / px_per_um
+            data[var].units = 'µm'
 
-    # create data
-    ds = np.DataSource(None)
-    f = ds.open(fspath(fpath), "rt")
-    axis0 = []
-    arr = []
-    attrs = {}
+    dtype = "image" if "x" in data.variable_names else "spectralprofile"
+    data.attrs.update(dtype=dtype)
 
-    line0 = f.readline().strip()[:-1]
-    line0 = [float(x) for x in line0.split(",")]  # TODO: robust to space, tab, comma
-    axis0.append(line0.pop(0))
-    arr.append(line0)
-    
-    def get_frames(f, arr, axis0):
-        axis0_written = False
-        while True:
-            line = f.readline().strip()[:-1]
-            if len(line) == 0:
-                break
-            else:
-                line = [float(x) for x in line.split(",")]
-                # signature of new frames is restart of axis0
-                if not axis0_written and (line[0] == axis0[0]):
-                    axis0_written = True
-                if axis0_written:
-                    line.pop(0)
-                else:
-                    axis0.append(line.pop(0))
-                arr.append(line)
-        return arr, axis0
+    if "wl" in data.variable_names:
+        data["wl"].attrs['label'] = "wavelength (nm)" if data["wl"].units == "nm" else "wavenumber (cm-1)"
 
-    arr, axis0 = get_frames(f, arr, axis0)
-    nframes = len(arr) // len(axis0)
-
-    i = 0
-    while i < 3:
-        line = f.readline().strip()
-        if len(line) == 0:
-            i += 1
-        else:
-            try:
-                key, val = line.split(":", 1)
-            except ValueError:
-                pass
-            else:
-                attrs[key.strip()] = val.strip()
-
-    f.close()
-
-    #create data object
-    arr = np.array(arr)
-    axis0 = np.array(axis0)
-    data = wt.Data(name=name)
-    if float(attrs["Grating Groove Density (l/mm)"]) == 0:
-        xname = 'x'
-        dtype = 'image'
-        try:
-            axis0 = axis0/objective_lenses[objective_lens]
-            xunits = 'µm'
-        except KeyError:
-            xunits = 'px'
+    if data.sig.units == "Hz":
+        data.sig.label = "intensity (cps)"
     else:
-        xname = 'wl'
-        xunits = 'nm'
-        dtype = 'spectralprofile'
-        
-    axis1 = np.arange(arr.shape[-1])
-    yname='y'
-    try:
-        axis1 = axis1/objective_lenses[objective_lens]
-        yunits = 'µm'
-    except KeyError:
-        yunits = 'px'
-    
-    axes = [xname, yname]
+        data.sig.label = "counts"
 
-    if nframes == 1:
-        arr = np.array(arr)
-        data.create_variable(name=xname, values=axis0[:, None], units=xunits)
-        data.create_variable(name=yname, values=axis1[None, :], units=yunits)
-    else:
-        frames = np.arange(nframes)
-        try:
-            ct = float(attrs["Kinetic Cycle Time (secs)"])
-            frames = frames*ct
-            tname = 't'
-            tunits = 's'
-        except KeyError:
-            tname = 'frame'
-            tunits = None
-        arr = np.array(arr).reshape(nframes, len(axis0), len(arr[0]))
-        data.create_variable(name=tname, values=frames[:, None, None], units=tunits)
-        data.create_variable(name=xname, values=axis0[None, :, None], units=xunits)
-        data.create_variable(name=yname, values=axis1[None, None, :], units=yunits)
-        axes = [tname] + axes
-
-    if xname=='wl':
-        if xunits=='nm':
-            data[xname].attrs['label'] = "wavelength (nm)"
-        if xunits=='wn':
-            data[xname].attrs['label'] = "wavenumber (cm-1)"
-    if xname=='x':
-        data[xname].attrs['label'] = "x (µm)"
-    if yname=='y':
-        data[yname].attrs['label'] = "y (µm)"
-
-    data.transform(*axes)
-    if cps:
-        try:
-            arr = arr/float(attrs["Exposure Time (secs)"])
-        except KeyError:
-            pass
-        try:
-            arr = arr/int(attrs["Number of Accumulations"])
-        except KeyError:
-            pass
-
-    data.create_channel(name='sig', values=arr, signed=False)
-    if cps:
-        data['sig'].attrs['label'] = "intensity (cps)"
-    else:
-        data['sig'].attrs['label'] = "counts"
-
-    for key, val in attrs.items():
-        data.attrs[key] = val
-
-    # finish
-    print("data created at {0}".format(data.fullpath))
-    print("  axes: {0}".format(data.axis_names))
-    print("  shape: {0}".format(data.shape))
-    data.attrs['dtype']=dtype
 
     return data
-