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.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']).as_matrix()
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.dot(where, 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, _ = np.dot(lookup_values, 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, _ = np.dot(xyzw, trans) # get hardware coordinates
if zh_travel:
self.Z.goto(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()