Big changes

Big changes

- renamed pycorn class object to pc_res3 (v3-results)
- renamed uvplotter to pycorn-bin
- new plotting system creates a single merged plot with 2 extra y-axes
- not all functionality of original pycorn-script re-implemented in new
script yet
- more changes soon

Author: pyahmed

examplescripts/pycorn-bin.py

@@ -0,0 +1,217 @@
+import argparse
+# from pathlib import Path
+
+from mpl_toolkits.axes_grid1 import host_subplot
+import mpl_toolkits.axisartist as AA
+import matplotlib.pyplot as plt
+# ^^^ = from matplotlib.pyplot import axvline, savefig, subplots, annotate
+
+from pycorn import pc_res3
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument("inp_res",
+                    help="Input .res file(s)",
+                    nargs='+',
+                    metavar="<file>.res")
+parser.add_argument("-e", "--ext", default='.pdf',
+                    help="Image type to use, e.g. 'jpg', 'png', 'eps', or 'pdf' (default: pdf)")
+parser.add_argument("--xmin", default=None, type=float,
+                    help="Lower bound on the x-axis")
+parser.add_argument("--xmax", default=None, type=float,
+                    help="Upper bound on the x-axis")
+parser.add_argument("--dpi", default=None, type=int,
+                    help="DPI (dots per inch) for raster images (png, jpg, etc.)")
+parser.add_argument("--par1", default=None, type=str,
+                    help="First parasite")
+parser.add_argument("--par2", default=None, type=str,
+                    help="Second parasite")
+
+
+
+args = parser.parse_args()
+
+
+def mapper(min_val, max_val, perc):
+    '''
+    calculate relative position in delta min/max
+    '''
+    x = abs(max_val - min_val) * perc
+    if min_val < 0:
+        return (x - abs(min_val))
+    else:
+        return (x + min_val)
+
+
+def expander(min_val, max_val, perc):
+    '''
+    expand -/+ direction of two values by a percentage of their delta
+    '''
+    delta = abs(max_val - min_val)
+    x = delta * perc
+    return (min_val - x, max_val + x)
+
+
+def xy_data(inp):
+    '''
+    Takes a data block and returns two lists with x- and y-data
+    '''
+    x_data = [x[0] for x in inp]
+    y_data = [x[1] for x in inp]
+    return x_data, y_data
+
+
+def uvdata(inp):
+    '''
+    helps in finding the useful data
+    '''
+    UV_blocks = [i for i in inp if i.startswith('UV') or i.endswith('nm')]
+    for i in UV_blocks:
+        if i.endswith("_0nm"):
+            UV_blocks.remove(i)
+
+
+def smartscale(inp):
+    '''
+    input is the entire fdata block
+    checks user input/fractions to determine scaling of x/y-axis
+    returns min/max for x/y
+    '''
+    UV_blocks = [i for i in inp.keys() if i.startswith('UV') and not i.endswith('_0nm')]
+    uv1_data = inp[UV_blocks[0]]['data']
+    uv1_x, uv1_y = xy_data(uv1_data)
+    try:
+        uv2_data = inp[UV_blocks[1]]['data']
+        uv2_x, uv2_y = xy_data(uv2_data)
+        uv3_data = inp[UV_blocks[2]]['data']
+        uv3_x, uv3_y = xy_data(uv3_data)
+    except:
+        KeyError
+        uv2_data = None
+        uv3_data = None
+    frac_delta = []
+    try:
+        frac_data = inp['Fractions']['data']
+        frac_x, frac_y = xy_data(frac_data)
+        frac_delta = [abs(a - b) for a, b in zip(frac_x, frac_x[1:])]
+        frac_delta.append(frac_delta[-1])
+    except:
+        KeyError
+        frac_data = None
+    if args.xmin:
+        plot_x_min = args.xmin
+    else:
+        if frac_data:
+            plot_x_min = frac_data[0][0]
+        else:
+            plot_x_min = uv1_x[0]
+    if args.xmax:
+        plot_x_max = args.xmax
+    else:
+        if frac_data:
+            plot_x_max = frac_data[-1][0] + frac_delta[-1]*2 # recheck
+        else:
+            plot_x_max = uv1_x[-1]
+    if plot_x_min > plot_x_max:
+        print("Warning: xmin bigger than xmax - adjusting...")
+        plot_x_min = uv1_x[0]
+    if plot_x_max < plot_x_min:
+        print("Warning: xmax smaller than xmin - adjusting...")
+        plot_x_max = uv1_x[-1]
+    # optimize y_scaling
+    min_y_values = []
+    max_y_values = []
+    for i in UV_blocks:
+        tmp_x, tmp_y = xy_data(inp[i]['data'])
+        range_min_lst = [abs(a - plot_x_min) for a in tmp_x]
+        range_min_idx = range_min_lst.index(min(range_min_lst))
+        range_max_lst = [abs(a - plot_x_max) for a in tmp_x]
+        range_max_idx = range_max_lst.index(min(range_max_lst))
+        values_in_range = tmp_y[range_min_idx:range_max_idx]
+        min_y_values.append(min(values_in_range))
+        max_y_values.append(max(values_in_range))
+    plot_y_min_tmp = min(min_y_values)
+    plot_y_max_tmp = max(max_y_values)
+    plot_y_min, plot_y_max = expander(plot_y_min_tmp, plot_y_max_tmp, 0.085)
+    return plot_x_min, plot_x_max, plot_y_min, plot_y_max
+
+def plotterX(inp,fname):
+    plot_x_min, plot_x_max, plot_y_min, plot_y_max = smartscale(inp)
+    host = host_subplot(111, axes_class=AA.Axes)
+    host.set_xlabel("Elution volume (ml)")
+    host.set_ylabel("Absorbance (mAu)")
+    host.set_xlim(plot_x_min, plot_x_max)
+    host.set_ylim(plot_y_min, plot_y_max)
+    for i in inp.keys():
+        if i.startswith('UV') and not i.endswith('_0nm'):
+            x_dat, y_dat = xy_data(inp[i]['data'])
+            print("Plotting: " + inp[i]['data_name'])
+            stl = styles[i[:4]]
+            p0, = host.plot(x_dat, y_dat, label=inp[i]['data_name'], color=stl['color'],
+                            ls=stl['ls'], lw=stl['lw'],alpha=stl['alpha'])
+    if args.par1:
+        par1_inp = args.par1
+        par1 = host.twinx()
+        par1_data = inp[par1_inp]
+        stl = styles[par1_inp]
+        par1.set_ylabel(par1_data['data_name'] + " (" + par1_data['unit'] + ")", color=stl['color'])
+        x_dat_p1, y_dat_p1 = xy_data(par1_data['data'])
+        p1_ymin, p1_ymax = expander(min(y_dat_p1), max(y_dat_p1), 0.085)
+        par1.set_ylim(p1_ymin, p1_ymax)
+        print("Plotting: " + par1_data['data_name'])
+        p1, = par1.plot(x_dat_p1, y_dat_p1, label=par1_data['data_name'], color=stl['color'],
+                        ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+    if args.par2:
+        par2_inp = args.par2
+        par2 = host.twinx()
+        offset = 60
+        new_fixed_axis = par2.get_grid_helper().new_fixed_axis
+        par2.axis["right"] = new_fixed_axis(loc="right", axes=par2, offset=(offset, 0))  
+        par2.axis["right"].toggle(all=True)
+        par2_data = inp[par2_inp]
+        stl = styles[par2_inp]
+        par2.set_ylabel(par2_data['data_name'] + " (" + par2_data['unit'] + ")", color=stl['color'])
+        x_dat_p2, y_dat_p2 = xy_data(par2_data['data'])
+        p2_ymin, p2_ymax = expander(min(y_dat_p2), max(y_dat_p2), 0.075)
+        par2.set_ylim(p2_ymin, p2_ymax)
+        print("Plotting: " + par2_data['data_name'])
+        p2, = par2.plot(x_dat_p2, y_dat_p2, label=par2_data['data_name'], color=stl['color'],
+                        ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+    try:
+        frac_data = inp['Fractions']['data']
+        frac_x, frac_y = xy_data(frac_data)
+        frac_delta = [abs(a - b) for a, b in zip(frac_x, frac_x[1:])]
+        frac_delta.append(frac_delta[-1])
+        frac_y_pos = mapper(host.get_ylim()[0], host.get_ylim()[1], 0.015)
+        for i in frac_data:
+            host.axvline(x=i[0], ymin=0.065, ymax=0.0, color='r', linewidth=0.85)
+            host.annotate(str(i[1]), xy=(i[0] + frac_delta[frac_data.index(i)] * 0.55, frac_y_pos),
+                         horizontalalignment='center', verticalalignment='bottom', size=8, rotation=90)
+    except:
+        KeyError
+    host.set_xlim(plot_x_min, plot_x_max)
+    host.legend(fontsize=8, fancybox=True, labelspacing=0.4)
+    plt.title(fname, loc='left')
+    internal_run_name = str(inp['Logbook']['run_name'])
+    plot_file = fname[:-4] + "_" + internal_run_name + "_plot" + args.ext
+    plt.savefig(plot_file, bbox_inches='tight', dpi=args.dpi)
+    print("Plot saved to: " + plot_file)
+#4e62ff
+styles = {'UV':{'color': '#1919FF', 'lw': 1.6, 'ls': "-", 'alpha':1.0},
+'UV1_':{'color': '#1919FF', 'lw': 1.6, 'ls': "-", 'alpha':1.0},
+'UV2_':{'color': '#e51616', 'lw': 1.4, 'ls': "-", 'alpha':1.0},
+'UV3_':{'color': '#c73de6', 'lw': 1.2, 'ls': "-", 'alpha':1.0},
+'Cond':{'color': '#62181A', 'lw': 1.4, 'ls': "-", 'alpha':0.75},
+'Conc':{'color': '#0F990F', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
+'Pres':{'color': '#3E1719', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
+'Temp':{'color': '#e04730', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
+'Inje':{'color': '#d56d9d', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
+'pH':{'color': '#0C7F7F', 'lw': 1.0, 'ls': "-", 'alpha':0.75},}
+
+def main2():
+    for fname in args.inp_res:
+        fdata = pc_res3(fname)
+        fdata.load()
+        plotterX(fdata, fname)
+
+main2()