Source code for acqpack.autosampler

import numpy as np
import pandas as pd

import utils as ut

[docs]class Autosampler: """ A high-level wrapper that coordinates XY and Z axes to create an autosampler. Incorporates a deck. """ def __init__(self, z, xy): # TODO: ditch frames; just have position_tables, each of which stores should transforms be a property of the position table? self.frames = pd.DataFrame(index=['trans', 'position_table']) self.add_frame('hardware') self.zh_travel = 0 self.Z = z # must be initialized first!!! (avoid collisions) self.XY = xy
[docs] def add_frame(self, name, trans=np.eye(4,4), 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) xyzw 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 (4,4) assert(trans.shape==(4,4)) # check size assert(np.array_equal(np.linalg.norm(trans[:-1,:-1]), np.linalg.norm(np.eye(3,3)))) # Frob norm rotation invariant (no scaling) assert(trans[-1,-1] != 0) # cannot be singular matrix # position_table: DataFrame with x,y,z OR None if isinstance(position_table, pd.DataFrame): assert(set(list('xyz')).issubset(position_table.columns)) # contains 'x','y','z' columns else: assert(position_table is None) self.frames[name] = None self.frames[name].trans = trans self.frames[name].position_table = position_table
# ref_frame gives reference frame; its offset is ignored
[docs] def add_plate(self, name, filepath, ref_frame='deck'): """ TODO: UNDER DEVELOPMENT """ # move to bottom of first well, i.e. plate origin (using GUI) # store offset (translation) offset = self.where() # hardware_xyz - plate_xyz (0,0,0) # determine transform trans = self.frames[ref_frame].copy() trans[-1] = offset # add position_table - either: # A) add from file while True: filepath = raw_input('Enter filepath to plate position_table:') try: position_table = ut.read_delim_pd(filepath) break except IOError: print 'No file:', filepath # add frame self.add_frame(name, trans, position_table)
[docs] def where(self, frame=None): """ Retrieves current hardware (x,y,z). 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() + self.Z.where() if frame is not None: where += (1,) x, y, z, _ = tuple(, np.linalg.inv(self.frames[frame].trans))) where = x, y, z return where
[docs] def home(self): """ Homes Z axis, then XY axes. """ self.Z.home() self.XY.home_xy()
# TODO: if no columns specified, transform provided XYZ to hardware coordinates. # TODO: default frame?
[docs] def goto(self, frame, lookup_columns, lookup_values, zh_travel=0): """ Finds lookup_values in lookup_columns of frame's position_list; retrieves corresponding X,Y,Z. Transforms X,Y,Z to hardware X,Y,Z by frame's transform. Moves to hardware X,Y,Z, taking into account zh_travel. :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 :param zh_travel: (float) hardware height at which to travel """ trans, position_table = self.frames[frame] if lookup_columns=='xyz': lookup_values = tuple(lookup_values) + (1,) xh, yh, zh, _ =, trans) else: xyz = tuple(ut.lookup(position_table, lookup_columns, lookup_values)[['x', 'y', 'z']].iloc[0]) xyzw = xyz + (1,) # concatenate for translation xh, yh, zh, _ =, trans) # get hardware coordinates if zh_travel>0: self.Z.goto(zh_travel) elif self.zh_travel>0: self.Z.goto(self.zh_travel) else: self.Z.home() self.XY.goto_xy(xh, yh) self.Z.goto(zh)
[docs] def exit(self): """ Send exit command to XY and Z """ self.XY.exit() self.Z.exit()