Source code for acqpack.fractioncollector

import numpy as np
import pandas as pd

import utils as ut

[docs]class FractionCollector: """ A high-level wrapper around an XY stage. """ def __init__(self, xy): self.frames = pd.DataFrame(index=['trans', 'position_table']) self.add_frame('hardware') self.XY = xy
[docs] def add_frame(self, name, trans=np.eye(3,3), position_table=None): """ Adds coordinate frame. Frame requires affine transform to hardware coordinates; position_table optional. :param name: (str) the name to be given to the frame (e.g. hardware) :param trans: (np.ndarray <- str) xyw affine transform matrix; if string, tries to load delimited file :param position_table: (None | pd.DataFrame <- str) position_table; if string, tries to load delimited file """ if isinstance(trans, str): trans = ut.read_delim_pd(trans).select_dtypes(['number']).values if isinstance(position_table, str): position_table = ut.read_delim_pd(position_table) assert(isinstance(trans, np.ndarray)) # trans: numpy array of shape (3,3) assert(trans.shape==(3,3)) # check size assert(np.array_equal(np.linalg.norm(trans[:-1,:-1]), np.linalg.norm(np.eye(2,2)))) # Frob norm rotation invariant (no scaling) assert(trans[-1,-1] != 0) # cannot be singular matrix # position_table: DataFrame with x,y OR None if isinstance(position_table, pd.DataFrame): assert(set(list('xy')).issubset(position_table.columns)) # contains 'x','y' columns else: assert(position_table is None) self.frames[name] = None self.frames[name].trans = trans self.frames[name].position_table = position_table
[docs] def where(self, frame=None): """ Retrieves current hardware (x,y). If frame is specified, transforms hardware coordinates into frame's coordinates. :param frame: (str) name of frame to specify transform (optional) :return: (tup) current position """ where = self.XY.where_xy() if frame is not None: where += (1,) x, y, _ = tuple(, np.linalg.inv(self.frames[frame].trans))) where = x, y return where
[docs] def home(self): """ Homes XY axes. """ self.XY.home_xy()
# TODO: if no columns specified, transform provided XY to hardware coordinates. # TODO: default frame?
[docs] def goto(self, frame, lookup_columns, lookup_values): """ Finds lookup_values in lookup_columns of frame's position_list; retrieves corresponding X,Y Transforms X,Y to hardware X,Y by frame's transform. Moves to hardware X,Y. :param frame: (str) frame that specifies position_list and transform :param lookup_columns: (str | list) column(s) to search in position_table :param lookup_values: (val | list) values(s) to find in lookup_columns """ trans, position_table = self.frames[frame] if lookup_columns=='xy': lookup_values = tuple(lookup_values) + (1,) xh, yh =, trans) else: xy = tuple(ut.lookup(position_table, lookup_columns, lookup_values)[['x', 'y']].iloc[0]) xyw = xy + (1,) # concatenate for translation xh, yh, _ =, trans) # get hardware coordinates self.XY.goto_xy(xh, yh)
[docs] def exit(self): """ Send exit command to XY. """ self.XY.exit()