DM_automation

This package's main purpose is to automatize the AO3000 and zygo measurements. It can:

• automatically take the influence function of each actuator on the DM through the zygo windows computer and send those files back to the linux DM.
• using data cubes of influence functions, reconstruct the surface of what a specific command from the DM would appear to be.
• convert .datx data into .fits data which is readable in python.

Almost all the tools to do this is created in convert_files.py. Adjust the file pathways accordingly w/in the convert_files.py class and in main.py. main.py initializes the convert_files class and sets up how you might want to take measurements.

How to configure

Step 1: Upload the measure.py file to the zygo computer. You can change the save path to whatever directory in the zygo computer that you desire; this will be where the data is temporarily saved.

       zygo1 = Zygo('C:\\Users\\zygo\\zygo_alicia\\zygo_rawdata')

Step 2: Upload the convert_files.py file to the linux DM computer. In the windows2linux method, change the file path to be the same as the zygo save path above.

       file_path = 'C:/Users/zygo/zygo_alicia/zygo_rawdata/'

While you're there, change the ssh.exec_command to the path to your measure.py file on the zygo computer.

       [a, b, c] = ssh.exec_command('python C:/Users/zygo/zygo_alicia/zygo_rawdata/measure.py ' + name)

Step 3: In the reset_zvals0 method, change the file_path to be the same as the zygo save path.

       file_path = 'C:/Users/zygo/zygo_alicia/zygo_rawdata/'

and in the ssh.exec_command

       [a, b, c] = ssh.exec_command('python C:/Users/zygo/zygo_alicia/zygo_rawdata/measure.py ' + name)

and in the sftp.get, change the first string to your zygo save path.

    sftp.get('C:\\Users\\zygo\\zygo_alicia\\zygo_rawdata\\z_init.datx', "/home/aorts/alicia/zygo_data/z_init.datx")

Step 4: Now, you need to decide where you want to save your .datx data on the linux DM computer. From now on, I'll refer to this directory as the retrieve_path. After going through data proccessing and getting rid of the piston, tip, tilt, your data will be saved to a new directory. This directory is called the save_path. In my case, my retrieve_path is "/home/aorts/alicia/zygo_rawdata/" and my save_path is "/home/aorts/alicia/zygo_data/".

Step 5: Now, I'm sorry that you have to do this, but you'll need to change all the paths accordingly. I'll do my best to walk you through everything.

In the reset_zvals0 method, change sftp.get's second string and the string in self._datx2py to save_path + 'z_init.datx'

    sftp.get('C:\\Users\\zygo\\zygo_alicia\\zygo_rawdata\\z_init.datx', "/home/aorts/alicia/zygo_rawdata/z_init.datx")
    h5data = self._datx2py("/home/aorts/alicia/zygo_data/z_init.datx")

In the get_zvals0 method, do the same as above. Change the string to save_path + 'z_init.datx'.

    h5data = self._datx2py('/home/aorts/alicia/zygo_data/z_init.datx')

In the analyze method, do the same as above, except this time with the self.show_h5data2 method.

    zvals0 = self.show_h5data2('/home/aorts/alicia/zygo_data/z_init.datx')

Finally, in read_mult_fits_file method, change completeName accordingly to your save_path. Replace

    completeName = '/home/aorts/alicia/zygo_data/infl_' + str(i + 1).zfill(4) + '.fits'

How to Use

Before you start using the class, there are a few house keeping things you should do.

dm = shm('dm64volt.im.shm') # creates connection to DM
retrieve_path = '/home/aorts/alicia/raw_data/' # this is where your .datx data will be saved
save_path = '/home/aorts/alicia/data/' # this is where you .fits files will be saved
convert = con(retrieve_path, save_path) # initialize class 
influence_functions = []
dm_cmd = np.zeros((64, 64))

active_actuators = convert.find_active_actuator()
zvals0 = convert.reset_zvals0()
nanmask = circular_aperture(0.9)(make_pupil_grid(zvals0.shape[0])).shaped
nanmask[nanmask == 0] = np.nan

main.py and main2.py are exmaples on how I've used this class.

Most useful methods:

• windows2linux grabs the file from zygo windows computer and saves it to the linux DM computer. Parameter file_name is what the new file will be named.
• subtract takes two .datx files and takes the difference between the two files.
• reset_zvals0 will take a measurement for all the actuators at zero.
• get_zvals0 will only retrieve the save zval file.
• read_fits_file will show a plt of the fits file path.
• read_mult_fits_files does the same as above, but for multiple fits files, given a start and stop index.

credit to kyohoon making/helping me make a majority of this code