Cctbx

cctbx

Source code in mfx/cctbx.py

class cctbx:
    def __init__(self):
        from mfx.macros import get_exp
        self.experiment = str(get_exp())


    def geom_refine(
        self,
        user: str,
        group: str,
        level: int = None,
        facility: str = "NERSC",
        exp: str = ''):
        """
        Launch CCTBX XFEL GUI.

        Parameters
        ----------
        user: str
            Username for computer account at facility.

        group: str
            The trial and rungroup number in the format 000_rg005.
            Default is newest trial_rungroup

        level: int
            The level of geometry refinement.
            0 = whole detector and 1 = individual detector panels.
            Default is to systematically do both.

        facility: str
            Default: "NERSC". Options: "S3DF, NERSC".

        exp: str
            Experiment number in format 'mfxp1047723'.
            If none selected default is the current experiment.

        debug: bool
            Default: False.

        """
        import logging
        import os

        if exp != '':
            experiment = exp
        else:
            experiment = self.experiment

        proc = [
            f"ssh -Yt {user}@s3dflogin "
            f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/geom_refine.py "
            f"-e {experiment} -f {facility} -g {group} -l {level} "
            ]

        logging.info(proc)

        if facility == 'NERSC':
            logging.warning(f"Have you renewed your token with sshproxy today?")
            token = input("(y/n)? ")

            if token.lower() == "n":
                self.sshproxy(user)

        os.system(proc[0])


    def average(
        self,
        user: str,
        run: int,
        facility: str = "NERSC",
        exp: str = '',
        debug: bool = False):
        """
        Launch CCTBX XFEL GUI.

        Parameters
        ----------
        user: str
            Username for computer account at facility.
        run: int
            Enter -r for the run number
        facility: str
            Default: "NERSC". Options: "S3DF, NERSC".
        exp: str
            Experiment number in format 'mfxp1047723'.
            If none selected default is the current experiment.
        debug: bool
            Default: False.
        """
        import logging
        import os
        import subprocess

        if exp != '':
            experiment = exp
        else:
            experiment = self.experiment

        proc = [
            f"ssh -Yt {user}@s3dflogin "
            f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/average.py "
            f"-e {experiment} -f {facility} -d {str(debug)} -r {run}"
            ]

        logging.info(proc)

        if facility == 'NERSC':
            logging.warning(f"Have you renewed your token with sshproxy today?")
            token = input("(y/n)? ")

            if token.lower() == "n":
                self.sshproxy(user)

        if debug:
            os.system(proc[0])
        else:
            subprocess.Popen(
                proc, shell=True,
                stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)


    def image_viewer(
        self,
        user: str,
        run: int,
        image_type: str,
        group: str = None,
        facility: str = "NERSC",
        exp: str = '',
        debug: bool = False):
        """
        Launch CCTBX XFEL GUI.

        Parameters
        ----------
        user: str
            username for computer account at facility.

        run: int
            Enter -r for the run number

        image_type: str
            Enter -t for type of image view

        group: str
            The trial and rungroup number in the format 000_rg005.
            Default is newest trial_rungroup

        facility: str
            Default: "NERSC". Options: "S3DF, NERSC".

        exp: str
            Experiment number in format 'mfxp1047723'.
            If none selected default is the current experiment.

        debug: bool
            Default: False.
        """
        import logging
        import os
        import subprocess

        if exp != '':
            experiment = exp
        else:
            experiment = self.experiment

        proc = [
            f"ssh -Yt {user}@s3dflogin "
            f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/image_viewer.py "
            f"-e {experiment} -f {facility} -d {str(debug)} -t {image_type} -r {run} -g {group}"
            ]

        logging.info(proc)

        if facility == 'NERSC':
            logging.warning(f"Have you renewed your token with sshproxy today?")
            token = input("(y/n)? ")

            if token.lower() == "n":
                self.sshproxy(user)

        if debug:
            os.system(proc[0])
        else:
            subprocess.Popen(
                proc, shell=True,
                stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)


    def sshproxy(
        self,
        user: str,
    ):

        """
        Launch sshproxy check for getting NERSC token if needed

        Parameters
        ----------
        user: str
            Username for computer account at facility.

        debug: bool
                Default: False.
        """
        import logging
        import os
        import subprocess
        logging.info(f"Creating new sshproxy token for {user}.")
        proc = [
            f"ssh -Yt {user}@s3dflogin "
            f"/sdf/group/lcls/ds/tools/mfx/scripts/cctbx/sshproxy.sh "
            f"-c cctbx -u {user}"
            ]

        logging.info(proc)

        os.system(proc[0])


    def xfel_gui(
        self,
        user: str,
        facility: str = "NERSC",
        exp: str  = '',
        debug: bool = False,
    ):
        """
        Launch CCTBX XFEL GUI.

        Parameters
        ----------
        user: str
            Username for computer account at facility.

        facility: str
            Default: "NERSC". Options: "S3DF, NERSC".

        exp: str
            Experiment number in format 'mfxp1047723'.
            If none selected default is the current experiment.

        debug: bool
            Default: False.
        """
        import logging
        import os
        import subprocess

        if exp != '':
            experiment = exp
        else:
            experiment = self.experiment

        proc = [
            f"ssh -Yt {user}@s3dflogin "
            f"/sdf/group/lcls/ds/tools/mfx/scripts/cctbx/cctbx.sh "
            f"{user} {experiment} {facility} 1 {str(debug)} "
            ]

        logging.info(proc)

        if facility == 'NERSC':
            logging.warning(f"Have you renewed your token with sshproxy today?")
            token = input("(y/n)? ")

            if token.lower() == "n":
                self.sshproxy(user)

        if debug:
            os.system(proc[0])
        else:
            subprocess.Popen(
                proc, shell=True,
                stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)


    def notch_check(self, user, runs=[]):
        import logging
        import subprocess
        import sys
        if len(runs) > 0:
            run_list = []
            for run in runs:
                run_list.append(f'{experiment}:{run}')
            logging.info(f'Selected runs: {run_list}')
            runlist = ' '
            runlist = runlist.join(run_list)
            logging.info(f'Selected runs: {runlist}')
        else:
            logging.warning(f'No selected runs. Program will exit.')
            sys.exit()

        proc = [
            f'ssh -YAC {user}@s3dflogin '
            f'/sdf/group/lcls/ds/tools/mfx/scripts/cctbx/cctbx_notch_check.sh "{self.runlist}"'
            ]

        logging.info(proc)

        subprocess.Popen(
            proc, shell=True, 
            stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)

average(user, run, facility='NERSC', exp='', debug=False)

Launch CCTBX XFEL GUI.

Parameters:

Name	Type	Description	Default
user	str	Username for computer account at facility.	required
run	int	Enter -r for the run number	required
facility	str	Default: "NERSC". Options: "S3DF, NERSC".	'NERSC'
exp	str	Experiment number in format 'mfxp1047723'. If none selected default is the current experiment.	''
debug	bool	Default: False.	False

Source code in mfx/cctbx.py

def average(
    self,
    user: str,
    run: int,
    facility: str = "NERSC",
    exp: str = '',
    debug: bool = False):
    """
    Launch CCTBX XFEL GUI.

    Parameters
    ----------
    user: str
        Username for computer account at facility.
    run: int
        Enter -r for the run number
    facility: str
        Default: "NERSC". Options: "S3DF, NERSC".
    exp: str
        Experiment number in format 'mfxp1047723'.
        If none selected default is the current experiment.
    debug: bool
        Default: False.
    """
    import logging
    import os
    import subprocess

    if exp != '':
        experiment = exp
    else:
        experiment = self.experiment

    proc = [
        f"ssh -Yt {user}@s3dflogin "
        f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/average.py "
        f"-e {experiment} -f {facility} -d {str(debug)} -r {run}"
        ]

    logging.info(proc)

    if facility == 'NERSC':
        logging.warning(f"Have you renewed your token with sshproxy today?")
        token = input("(y/n)? ")

        if token.lower() == "n":
            self.sshproxy(user)

    if debug:
        os.system(proc[0])
    else:
        subprocess.Popen(
            proc, shell=True,
            stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)

geom_refine(user, group, level=None, facility='NERSC', exp='')

Launch CCTBX XFEL GUI.

Parameters:

Name	Type	Description	Default
user	str	Username for computer account at facility.	required
group	str	The trial and rungroup number in the format 000_rg005. Default is newest trial_rungroup	required
level	int	The level of geometry refinement. 0 = whole detector and 1 = individual detector panels. Default is to systematically do both.	None
facility	str	Default: "NERSC". Options: "S3DF, NERSC".	'NERSC'
exp	str	Experiment number in format 'mfxp1047723'. If none selected default is the current experiment.	''
debug		Default: False.	required

Source code in mfx/cctbx.py

def geom_refine(
    self,
    user: str,
    group: str,
    level: int = None,
    facility: str = "NERSC",
    exp: str = ''):
    """
    Launch CCTBX XFEL GUI.

    Parameters
    ----------
    user: str
        Username for computer account at facility.

    group: str
        The trial and rungroup number in the format 000_rg005.
        Default is newest trial_rungroup

    level: int
        The level of geometry refinement.
        0 = whole detector and 1 = individual detector panels.
        Default is to systematically do both.

    facility: str
        Default: "NERSC". Options: "S3DF, NERSC".

    exp: str
        Experiment number in format 'mfxp1047723'.
        If none selected default is the current experiment.

    debug: bool
        Default: False.

    """
    import logging
    import os

    if exp != '':
        experiment = exp
    else:
        experiment = self.experiment

    proc = [
        f"ssh -Yt {user}@s3dflogin "
        f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/geom_refine.py "
        f"-e {experiment} -f {facility} -g {group} -l {level} "
        ]

    logging.info(proc)

    if facility == 'NERSC':
        logging.warning(f"Have you renewed your token with sshproxy today?")
        token = input("(y/n)? ")

        if token.lower() == "n":
            self.sshproxy(user)

    os.system(proc[0])

image_viewer(user, run, image_type, group=None, facility='NERSC', exp='', debug=False)

Launch CCTBX XFEL GUI.

Parameters:

Name	Type	Description	Default
user	str	username for computer account at facility.	required
run	int	Enter -r for the run number	required
image_type	str	Enter -t for type of image view	required
group	str	The trial and rungroup number in the format 000_rg005. Default is newest trial_rungroup	None
facility	str	Default: "NERSC". Options: "S3DF, NERSC".	'NERSC'
exp	str	Experiment number in format 'mfxp1047723'. If none selected default is the current experiment.	''
debug	bool	Default: False.	False

Source code in mfx/cctbx.py

def image_viewer(
    self,
    user: str,
    run: int,
    image_type: str,
    group: str = None,
    facility: str = "NERSC",
    exp: str = '',
    debug: bool = False):
    """
    Launch CCTBX XFEL GUI.

    Parameters
    ----------
    user: str
        username for computer account at facility.

    run: int
        Enter -r for the run number

    image_type: str
        Enter -t for type of image view

    group: str
        The trial and rungroup number in the format 000_rg005.
        Default is newest trial_rungroup

    facility: str
        Default: "NERSC". Options: "S3DF, NERSC".

    exp: str
        Experiment number in format 'mfxp1047723'.
        If none selected default is the current experiment.

    debug: bool
        Default: False.
    """
    import logging
    import os
    import subprocess

    if exp != '':
        experiment = exp
    else:
        experiment = self.experiment

    proc = [
        f"ssh -Yt {user}@s3dflogin "
        f"python /sdf/group/lcls/ds/tools/mfx/scripts/cctbx/image_viewer.py "
        f"-e {experiment} -f {facility} -d {str(debug)} -t {image_type} -r {run} -g {group}"
        ]

    logging.info(proc)

    if facility == 'NERSC':
        logging.warning(f"Have you renewed your token with sshproxy today?")
        token = input("(y/n)? ")

        if token.lower() == "n":
            self.sshproxy(user)

    if debug:
        os.system(proc[0])
    else:
        subprocess.Popen(
            proc, shell=True,
            stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)

sshproxy(user)

Launch sshproxy check for getting NERSC token if needed

Parameters:

Name	Type	Description	Default
user	str	Username for computer account at facility.	required
debug		Default: False.	required

Source code in mfx/cctbx.py

def sshproxy(
    self,
    user: str,
):

    """
    Launch sshproxy check for getting NERSC token if needed

    Parameters
    ----------
    user: str
        Username for computer account at facility.

    debug: bool
            Default: False.
    """
    import logging
    import os
    import subprocess
    logging.info(f"Creating new sshproxy token for {user}.")
    proc = [
        f"ssh -Yt {user}@s3dflogin "
        f"/sdf/group/lcls/ds/tools/mfx/scripts/cctbx/sshproxy.sh "
        f"-c cctbx -u {user}"
        ]

    logging.info(proc)

    os.system(proc[0])

xfel_gui(user, facility='NERSC', exp='', debug=False)

Launch CCTBX XFEL GUI.

Parameters:

Name	Type	Description	Default
user	str	Username for computer account at facility.	required
facility	str	Default: "NERSC". Options: "S3DF, NERSC".	'NERSC'
exp	str	Experiment number in format 'mfxp1047723'. If none selected default is the current experiment.	''
debug	bool	Default: False.	False

Source code in mfx/cctbx.py

def xfel_gui(
    self,
    user: str,
    facility: str = "NERSC",
    exp: str  = '',
    debug: bool = False,
):
    """
    Launch CCTBX XFEL GUI.

    Parameters
    ----------
    user: str
        Username for computer account at facility.

    facility: str
        Default: "NERSC". Options: "S3DF, NERSC".

    exp: str
        Experiment number in format 'mfxp1047723'.
        If none selected default is the current experiment.

    debug: bool
        Default: False.
    """
    import logging
    import os
    import subprocess

    if exp != '':
        experiment = exp
    else:
        experiment = self.experiment

    proc = [
        f"ssh -Yt {user}@s3dflogin "
        f"/sdf/group/lcls/ds/tools/mfx/scripts/cctbx/cctbx.sh "
        f"{user} {experiment} {facility} 1 {str(debug)} "
        ]

    logging.info(proc)

    if facility == 'NERSC':
        logging.warning(f"Have you renewed your token with sshproxy today?")
        token = input("(y/n)? ")

        if token.lower() == "n":
            self.sshproxy(user)

    if debug:
        os.system(proc[0])
    else:
        subprocess.Popen(
            proc, shell=True,
            stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)