latest changes as of 2024-06-07

Merge master into SLAB to add new functionalities

eco/acquisition/epics_data.py

@@ -14,7 +14,7 @@ import time
 class EpicsDaq:
     def __init__(
         self,
-        default_file_path="%s",
+        default_file_path="",
         elog=None,
         name=None,
         channel_list=None,

eco/acquisition/ioxos_slab.py

@@ -0,0 +1,276 @@
+import numpy as np
+import h5py
+from epics import PV
+import os
+import datetime
+from threading import Thread
+from time import sleep
+from pathlib import Path
+from .utilities import Acquisition
+import time
+from eco.elements.assembly import Assembly
+from eco.elements.adjustable import AdjustableFS
+from eco.epics.adjustable import AdjustablePv, AdjustablePvEnum
+
+class IoxosChannel(Assembly):
+    def __init__(
+        self,
+        pvbase = "SLAB-LSCP1-ESB1",
+        name=None,
+        ch=None,
+
+    ):
+        super().__init__(name=name)
+        self.pvbase = pvbase
+        self._append(AdjustablePv, self.pvbase + f":CH{ch}:BSTART_NEW", name = "bg_start", is_setting=True)
+        self._append(AdjustablePv, self.pvbase + f":CH{ch}:BEND_NEW", name = "bg_end", is_setting=True)
+        self._append(AdjustablePv, self.pvbase + f":CH{ch}:START_NEW", name = "sig_start", is_setting=True)
+        self._append(AdjustablePv, self.pvbase + f":CH{ch}:END_NEW", name = "sig_end", is_setting=True)
+        self._append(AdjustablePvEnum, self.pvbase + f":BOX_STAT{ch}", name = "boxcar_calculation", is_setting=True)
+        self._append(AdjustableFS, f"/sf/slab/config/eco/reference_values/ioxos_{name}_chopper_ch", name="chopper_ch", is_setting=True, default_value=0)
+        self._append(AdjustableFS, f"/sf/slab/config/eco/reference_values/ioxos_{name}_chopper_thr", name="chopper_thr", is_setting=True, default_value=1000)
+        self._append(AdjustableFS, f"/sf/slab/config/eco/reference_values/ioxos_{name}_chopper_inv", name="chopper_inv", is_setting=True, default_value=True)
+
+class Slab_Ioxos(Assembly):
+    def __init__(
+        self,
+        name=None,
+        pvbase = "SLAB-LSCP1-ESB1",
+    ):
+        super().__init__(name=name)
+        self.pvbase= pvbase        
+        self._append(AdjustablePv, self.pvbase + ":BOX_RESTART.PROC", name="restart", is_setting=False)
+        self._append(AdjustablePv, self.pvbase + ":BOX_SAMS_IN_ARRAY", name="samples", is_setting=True)
+        self._append(AdjustablePv, self.pvbase + ":BOX_BLOCKS_TO_SEND", name="blocks", is_setting=True)
+        self._append(AdjustablePvEnum, self.pvbase + ":BOX_INARRAY", name="active_channels", is_setting=True)
+        self._append(AdjustablePv, self.pvbase + ":BOX_FREQ", name="trigger_rate", is_setting=False)
+        self._append(AdjustablePv, self.pvbase + f":TRIGGER:MINACQINTERVAL:1", name = "trigger_waittime", is_setting=True)
+        self._append(AdjustablePv, "SLAB-CVME-ESB1:SYS_CPU_LOAD", name="cpu_load", is_setting=False, is_display=True)
+        self.samples(10)
+        self.blocks(0)
+        self.restart(1)
+        self.active_channels(7)
+        self.trigger_waittime(0)
+        self.data = PV("SLAB-LSCP1-ESB1:BOX_DATA", auto_monitor=True)
+        for ch in range(8):
+            self._append(IoxosChannel, pvbase=self.pvbase, name=f"ch{ch}", ch=ch, is_setting=False, is_display=False,)
+
+class Slab_Ioxos_Daq(Assembly):
+    def __init__(
+        self,
+        default_file_path="",
+        name=None,
+        ioxos = None,
+    ):
+        super().__init__(name=name)
+        self.ioxos = ioxos
+        self._append(AdjustableFS, "/sf/slab/config/eco/reference_values/ioxos_daq_single_shots", name="save_single_shots", is_setting=True)
+        self._done = False
+        self._default_file_path = default_file_path
+        self._N_acqs = 0
+        self._data = np.zeros((0,))
+        self._meta_len = 12
+
+        def cb_get_data(*args, **kwargs):
+            if self._N_acqs > 0:
+                d = kwargs["value"][self._meta_len:]
+                idx0 = self._data.shape[0]-self._N_acqs*d.shape[0]
+                idx1 = self._data.shape[0]-(self._N_acqs-1)*d.shape[0]
+                self._data[idx0:idx1] = d
+                self._N_acqs = self._N_acqs - 1
+        self.ioxos.data.add_callback(callback = cb_get_data)
+
+    def get_data(self, N_pulses=None):
+        
+        N_channels = 8
+        if N_pulses > 10:
+            N_acqs = N_pulses // 10
+        else:
+            N_pulses=10
+            N_acqs = 1
+        self._data=np.zeros((N_channels*N_pulses))
+        self._N_acqs = N_acqs
+        while(True):
+            if self._N_acqs == 0:
+                break
+            sleep(.001)
+        return self._data.reshape((N_pulses, N_channels)).T
+
+    def save_single(self, file_name, data):
+        if os.path.isfile(file_name):
+            print(f"!!! File {file_name} already exists, would you like to delete it?")
+            if input("(y/n)") == "y":
+                print(f"Deleting {file_name} .")
+                os.remove(file_name)
+            else:
+                return
+        N_channels = data.shape[0]
+        d = {f"ch{n}": data[n] for n in range(N_channels)}
+        np.savez_compressed(file_name, **d)
+        fp = Path(file_name)
+        fp.chmod(0o775)
+
+    def save_av(self, file_name, data, adjs_rb, adjs_name, N_pulses):
+        chopper_chs = [self.ioxos.__dict__[f"ch{n}"].chopper_ch() for n in range(8)]
+        chopper_thrs = [self.ioxos.__dict__[f"ch{n}"].chopper_thr() for n in range(8)]
+        chopper_invs = [self.ioxos.__dict__[f"ch{n}"].chopper_inv() for n in range(8)]
+        w = np.array([data[ch]<thr if inv else data[ch]>thr for ch, thr, inv in zip(chopper_chs, chopper_thrs, chopper_invs)])
+        d_av_on = np.mean(data, axis=1, where=w)
+        d_av_off = np.mean(data, axis=1, where=~w)
+        d_std_on = np.std(data, axis=1, where=w)
+        d_std_off = np.std(data, axis=1, where=~w)
+        d_npulses_on = np.sum(w, axis=1)
+        d_npulses_off = np.sum(~w, axis=1)
+        filename_av = file_name.split("_step")[0] + ".txt"
+        d = np.hstack([adjs_rb, d_av_on, d_av_off, d_std_on, d_std_off, d_npulses_on, d_npulses_off])
+        exists = os.path.isfile(filename_av)
+        with open(filename_av, "a") as f:
+            if exists:
+                np.savetxt(f,[d])
+            else:
+                head = [f"{n}, " for n in adjs_name]
+                head.extend([f"ch{n}_on, " for n in range(8)])
+                head.extend([f"ch{n}_off, " for n in range(8)])
+                head.extend([f"ch{n}_on_std, " for n in range(8)])
+                head.extend([f"ch{n}_off_std, " for n in range(8)])
+                head.extend([f"ch{n}_on_npulses, " for n in range(8)])
+                head.extend([f"ch{n}_off_npulses, " for n in range(8)])
+                header = "".join(head)
+                np.savetxt(f,[d],header=header)
+                fp = Path(filename_av)
+                fp.chmod(0o775)
+
+    def acquire(self, file_name=None, N_pulses=100, adjs_rb = [], adjs_name=[], default_path=True):
+
+        file_name += ".npz"
+        if default_path:
+            file_name = self._default_file_path + file_name
+        data_dir = Path(os.path.dirname(file_name))
+
+        if not data_dir.exists():
+            print(
+                f"Path {data_dir.absolute().as_posix()} does not exist, will try to create it..."
+            )
+            data_dir.mkdir(parents=True)
+            print(f"Tried to create {data_dir.absolute().as_posix()}")
+            data_dir.chmod(0o775)
+            print(f"Tried to change permissions to 775")
+
+        def acquire():
+            d = self.get_data(N_pulses = N_pulses)
+            self.save_av(file_name, d, adjs_rb, adjs_name, N_pulses)
+            if self.save_single_shots():
+                self.save_single(file_name=file_name, data=d)
+
+        return Acquisition(
+            acquire=acquire,
+            acquisition_kwargs={"file_names": [file_name], "N_pulses": N_pulses, "adjs_rb": adjs_rb, "adjs_name": adjs_name},
+            hold=False,
+        )
+
+    def wait_done(self):
+        self.check_running()
+        self.check_still_running()
+
+
+class Epicstools:
+    def __init__(
+        self,
+        default_channel_list={"listname": []},
+        default_file_path="%s",
+        elog=None,
+        name=None,
+        channel_list=None,
+    ):
+        self.name = name
+        self._default_file_path = default_file_path
+        self._default_channel_list = default_channel_list
+        self._elog = elog
+        self.channels = []
+        self.pulse_id = PV("SLAAR11-LTIM01-EVR0:RX-PULSEID")
+
+        if not channel_list:
+
+            print("No channels specified, using all lists instead.")
+            channel_list = []
+            for tlist in self._default_channel_list.values():
+                channel_list.extend(tlist)
+        else:
+            self.channel_list = channel_list
+        for channel in self.channel_list:
+            self.channels.append(PV(channel, auto_monitor=True))
+
+    def h5(self, fina=None, channel_list=None, N_pulses=None, queue_size=100):
+        channel_list = self.channel_list
+
+        if os.path.isfile(fina):
+            print("!!! File %s already exists, would you like to delete it?" % fina)
+            if input("(y/n)") == "y":
+                print("Deleting %s ." % fina)
+                os.remove(fina)
+            else:
+                return
+
+        data = []
+        counters = []
+        channels = self.channels
+        for channel in channels:
+            channelval = channel.value
+            if type(channelval) == np.ndarray:
+                shape = (N_pulses,) + channelval.shape
+                dtype = channelval.dtype
+            else:
+                shape = (N_pulses,)
+                dtype = type(channelval)
+            data.append(np.ndarray(shape, dtype=dtype))
+            counters.append(0)
+
+        def cb_getdata(ch=None, m=0, *args, **kwargs):
+            data[m][counters[m]] = kwargs["value"]
+            counters[m] = counters[m] + 1
+            if counters[m] == N_pulses:
+                ch.clear_callbacks()
+
+        for (m, channel) in enumerate(channels):
+            channel.add_callback(callback=cb_getdata, ch=channel, m=m)
+        while True:
+            sleep(0.005)
+            if np.mean(counters) == N_pulses:
+                break
+
+        f = h5py.File(name=fina, mode="w")
+        for (n, channel) in enumerate(channel_list):
+            dat = f.create_group(name=channel)
+            dat.create_dataset(name="data", data=data[n])
+            dat.create_dataset(
+                name="pulse_id", data=np.arange(N_pulses) + round(time.time() * 100)
+            )
+        return data
+
+    def acquire(self, file_name=None, Npulses=100, default_path=True):
+        file_name += ".h5"
+        if default_path:
+            file_name = self._default_file_path + file_name
+        data_dir = Path(os.path.dirname(file_name))
+
+        if not data_dir.exists():
+            print(
+                f"Path {data_dir.absolute().as_posix()} does not exist, will try to create it..."
+            )
+            data_dir.mkdir(parents=True)
+            print(f"Tried to create {data_dir.absolute().as_posix()}")
+            data_dir.chmod(0o775)
+            print(f"Tried to change permissions to 775")
+
+        def acquire():
+            self.h5(fina=file_name, N_pulses=Npulses)
+
+        return Acquisition(
+            acquire=acquire,
+            acquisition_kwargs={"file_names": [file_name], "Npulses": Npulses},
+            hold=False,
+        )
+
+    def wait_done(self):
+        self.check_running()
+        self.check_still_running()

eco/acquisition/scan.py

@@ -9,6 +9,7 @@ import colorama
 from ..elements.adjustable import DummyAdjustable
 from IPython import get_ipython
 from .daq_client import Daq
+from .ioxos_slab import Slab_Ioxos_Daq
 from eco.elements.assembly import Assembly
 from rich.progress import Progress
 
@@ -215,6 +216,8 @@ class Scan:
                 acq = ctr.acquire(
                     file_name=fina, Npulses=self.pulses_per_step[0], acq_pars=acq_pars
                 )
+            elif isinstance(ctr, Slab_Ioxos_Daq):
+                acq = ctr.acquire(file_name=fina, N_pulses=self.pulses_per_step[0], adjs_rb=readbacks_step, adjs_name=[adj.name for adj in self.adjustables]) 
             else:
                 acq = ctr.acquire(file_name=fina, Npulses=self.pulses_per_step[0])
             acs.append(acq)

eco/devices_general/detectors.py

@@ -2,8 +2,10 @@ import numpy as np
 from epics import caget
 from epics import PV
 from eco.epics.utilities_epics import EnumWrapper
-
-from bsread import source, SUB
+try:
+    from bsread import source, SUB
+except:
+    pass
 import subprocess
 import h5py
 from time import sleep

eco/devices_general/temperature_controllers.py

@@ -0,0 +1,49 @@
+from ..aliases import Alias, append_object_to_object
+from ..elements.adjustable import AdjustableVirtual, AdjustableGetSet, value_property
+from ..epics.adjustable import AdjustablePv, AdjustablePvEnum
+from ..elements.assembly import Assembly
+class Lakeshore_331(Assembly):
+    def __init__(self, pvname, name=None):
+        super().__init__(name=name)
+        self.pvname = pvname
+        self._append(
+            AdjustablePv,
+            pvsetname = "SLAB-LLS-UNIT1:HT-LVL_RBV",
+            pvreadbackname = "SLAB-LLS-UNIT1:HT-LVL_RBV",
+            accuracy = 0.5,
+            name="heater_level",
+            is_display=True,
+            is_setting=False,
+        )
+        self._append(
+            AdjustablePv,
+            pvsetname = f"{self.pvname}:TEMP.VAL",
+            pvreadbackname = f"{self.pvname}:TEMP_RBV",
+            accuracy = 0.5,
+            name="temperature",
+            is_display=True,
+            is_setting=True,
+        )
+        self._append(
+            AdjustablePvEnum,
+            pvname = self.pvname + ":CONN",
+            name="connect",
+            is_setting=True,
+            is_display=False,
+        )
+        self._append(
+            AdjustablePvEnum,
+            pvname = self.pvname + ":HT-RNG_RBV",
+            pvname_set = self.pvname + ":HT-RNG",
+            name="heater_range",
+            is_setting=True,
+            is_display=True,
+        )
+        self._append(
+            AdjustablePvEnum,
+            pvname = self.pvname + ":MODE_RBV",
+            pvname_set = self.pvname + ":MODE",
+            name="operation",
+            is_setting=True,
+            is_display=True,
+        )

eco/elements/adjustable.py

@@ -795,7 +795,7 @@ class Tweak:
                 self.thread = None
 
             def print(self):
-                if self.thread and self.thread.isAlive():
+                if self.thread and self.thread.is_alive():
                     return
                 else:
                     self.thread = Thread(target=self.print_foo)

eco/sample_env/environment_sensors.py

@@ -0,0 +1,41 @@
+from ..epics.detector import DetectorPvDataStream
+from ..elements.assembly import Assembly
+
+class Env_Sensors(Assembly):
+    def __init__(self, name=None):
+        super().__init__(name=name)
+        self._append(
+            DetectorPvDataStream,
+            "SLAB-LI2C01_CH1:TEMP",
+            name="sens1_temperature",
+        )
+        self._append(
+            DetectorPvDataStream,
+            "SLAB-LI2C01_CH1:HUMIREL",
+            name="sens1_humidity",
+        )
+        self._append(
+            DetectorPvDataStream, 
+            "SLAB-LI2C01_CH1:PRES", 
+            name="sens1_pressure"
+        )
+        self._append(
+            DetectorPvDataStream,
+            "SLAB-LI2C01_CH2:TEMP",
+            name="sens2_temperature",
+        )
+        self._append(
+            DetectorPvDataStream,
+            "SLAB-LI2C01_CH2:HUMIREL",
+            name="sens2_humidity",
+        )
+        self._append(
+            DetectorPvDataStream, 
+            "SLAB-LI2C01_CH2:PRES", 
+            name="sens2_pressure"
+        )
+        self._append(
+            DetectorPvDataStream,
+            "SLAB-LI2C01_CH3:TEMP",
+            name="pt100_temperature",
+        )

eco/slab/__init__.py

@@ -0,0 +1,2 @@
+from .slab import *
+

eco/slab/slab.py

@@ -0,0 +1,263 @@
+from ..utilities.config import Namespace, Configuration
+from ..aliases import NamespaceCollection
+import pyttsx3
+from ..utilities.path_alias import PathAlias
+import os
+from pathlib import Path
+import shutil
+from eco.elements.adj_obj import AdjustableObject
+from eco.elements.adjustable import AdjustableFS
+
+### set pgroup from user input ###
+exp_path = Path("/sf/slab/exp/")
+exps = [[p.stem, p.resolve().stem] for p in exp_path.glob("*")]
+idx = ''
+input_message = "Select the pgroup of the experiment:\n"
+for index, (expname, pgroup) in enumerate(exps):
+    input_message += f'{index:2}) {expname:10} ({pgroup})\n'
+input_message += 'Your choice:'
+while idx not in range(len(exps)):
+    try:
+        idx = int(input(input_message))
+    except:
+        continue
+print(f'Selected experiment: {exps[idx][0]} {(exps[idx][1])}')
+pgroup = exps[idx][1]
+
+os.sys.path.insert(0,"/sf/slab/config/src/python/py_scilog")
+_eco_lazy_init = False
+
+cfg_path = Path(f"/sf/slab/config/eco/{pgroup}_slab_config_eco.json")
+if not cfg_path.exists():
+    shutil.copy2("/sf/slab/config/eco/slab_config_eco.json", cfg_path.as_posix())
+_config = AdjustableFS(
+    cfg_path.as_posix(), name="_config"
+)
+
+path_aliases = PathAlias()
+namespace = Namespace(
+    name="slab", root_module=__name__, alias_namespace=NamespaceCollection().slab
+)
+namespace.alias_namespace.data = []
+namespace.append_obj(AdjustableObject, _config, name="config")
+# Adding stuff that might be relevant for stuff configured below (e.g. config)
+config.pgroup(pgroup)
+
+namespace.append_obj(
+    "set_global_memory_dir",
+    "/sf/slab/config/eco/memory",
+    module_name="eco.elements.memory",
+    name="path_memory",
+)
+
+namespace.append_obj(
+    "DataApi",
+    name="archiver",
+    module_name="eco.dbase.archiver",
+    pv_pulse_id="SARES20-CVME-01-EVR0:RX-PULSEID",
+    add_to_cnf=True,
+    lazy=False,
+)
+
+namespace.append_obj(
+    "Slab_Ioxos",
+    name="ioxos",
+    module_name="eco.acquisition.ioxos_slab",
+    pvbase="SLAB-LSCP1-ESB1",
+    lazy=True,
+)
+
+#f"/sf/bernina/data/{config['pgroup']}/res/",
+namespace.append_obj(
+    "Slab_Ioxos_Daq",
+    name="daq",
+    module_name="eco.acquisition.ioxos_slab",
+    default_file_path=f'/sf/slab/data/{config.pgroup()}/res/',
+    #default_file_path=f'/sf/slab/config/eco/test_acq/',
+    ioxos=ioxos,
+    lazy=True,
+)
+
+
+## Utilities
+namespace.append_obj(
+    "Run_Table2",
+    name="run_table",
+    module_name="eco.utilities.runtable",
+    exp_id= config.pgroup(),
+    folder_id= "1n10Sfib-P9xqUhIQ0UuYUEkb_DpY3pcd",
+    exp_path= f"/sf/slab/data/{config.pgroup()}/res/run_table/",
+    #exp_path= f"/sf/slab/config/eco/test_acq/",
+    devices= "slab",
+    keydf_fname= "/sf/slab/config/eco/run_table/gspread_keys.pkl",
+    cred_fname= "/sf/slab/config/eco/run_table/pandas_push",
+    gsheet_key_path= "/sf/slab/config/eco/run_table/run_table_gsheet_keys", 
+    lazy=True,
+)
+
+
+namespace.append_obj(
+    "Lakeshore_331",
+    pvname = "SLAB-LLS-UNIT1",
+    name = "cryostat_janis",
+    module_name="eco.devices_general.temperature_controllers",
+    lazy=True,
+)
+   
+namespace.append_obj(
+    "Env_Sensors",
+    name="env_sensors",
+    module_name="eco.sample_env.environment_sensors",
+    lazy=True,
+)
+
+## 800pp setup stages
+namespace.append_obj(
+    "SmaractStreamdevice",
+    pvname = f"SLAB-LMTS-LAM11",
+    accuracy=1e-3,
+    name="delay_800pp_stg",
+    module_name="eco.devices_general.motors",
+    offset_file=f"/sf/slab/config/eco/reference_values/smaract_delay_800pp_stg",
+    lazy=True,
+)
+namespace.append_obj(
+    "DelayTime",
+    module_name="eco.loptics.bernina_laser",
+    stage=delay_800pp_stg,
+    name="delay_800pp",
+)
+namespace.append_obj(
+    "MotorRecord",
+    module_name="eco.devices_general.motors",
+    pvname="SLAB-LMOT-M002:MOT",
+    name="rotation_wp",
+    lazy=True,
+)
+
+
+## Mid-IR setup stages
+namespace.append_obj(
+    "MotorRecord",
+    module_name="eco.devices_general.motors",
+    pvname="SLAB-LMOT-M001:MOT",
+    name="delay_mirpp_stg",
+    lazy=True,
+)
+namespace.append_obj(
+    "DelayTime",
+    module_name="eco.loptics.bernina_laser",
+    stage=delay_mirpp_stg,
+    name="delay_mirpp",
+)
+
+## Other stages
+
+namespace.append_obj(
+    "MotorRecord",
+    module_name="eco.devices_general.motors",
+    pvname="SLAB-LMOT-M003:MOT",
+    name="rotation_micos_1",
+    lazy=True,
+)
+namespace.append_obj(
+    "MotorRecord",
+    module_name="eco.devices_general.motors",
+    pvname="SLAB-LMOT-M004:MOT",
+    name="rotation_micos_2",
+    lazy=True,
+)
+
+
+
+## Scan callback functions
+
+def _message_end_scan(scan):
+    e = pyttsx3.init()
+    e.say(f"Finished run {scan.run_number}.")
+    e.runAndWait()
+    e.stop()
+
+
+callbacks_start_scan = []
+callbacks_end_scan = []
+
+elog=None
+def _create_metadata_structure_start_scan(scan, run_table=run_table, elog=elog):
+    runname = os.path.basename(scan.fina).split(".")[0]
+    runno = int(runname.split("run")[1].split("_")[0])
+    metadata = {
+        "type": "scan",
+        "name": runname.split("_", 1)[1],
+        "scan_info_file": scan.scan_info_filename,
+    }
+    for n, adj in enumerate(scan.adjustables):
+        nname = None
+        nId = None
+        if hasattr(adj, "Id"):
+            nId = adj.Id
+        if hasattr(adj, "name"):
+            nname = adj.name
+
+        metadata.update(
+            {
+                f"scan_motor_{n}": nname,
+                f"from_motor_{n}": scan.values_todo[0][n],
+                f"to_motor_{n}": scan.values_todo[-1][n],
+                f"id_motor_{n}": nId,
+            }
+        )
+    metadata.update(
+        {
+            "steps": len(scan.values_todo),
+            "pulses_per_step": scan.pulses_per_step,
+            "counters": [daq.name for daq in scan.counterCallers],
+        }
+    )
+
+    try:
+        try:
+            metadata.update({"scan_command": get_ipython().user_ns["In"][-1]})
+        except:
+            print("Count not retrieve ipython scan command!")
+
+        message_string = f'Acquisition run {runno}: {metadata["name"]}\n'
+        if "scan_command" in metadata.keys():
+            message_string += metadata["scan_command"] + "\n"
+        message_string += metadata["scan_info_file"] + "\n"
+        scan._elog_id = elog.post(
+            message_string, Title=f'Run {runno}: {metadata["name"]}'
+        )
+        metadata.update({"elog_message_id": scan._elog_id})
+        metadata.update({"elog_post_link": scan._elog._log._url + str(scan._elog_id)})
+    except:
+        print("elog posting failed")
+    try:
+        run_table.append_run(runno, metadata=metadata)
+    except:
+        print("WARNING: issue adding data to run table")
+
+
+# <<<< Extract for run table and elog
+callbacks_start_scan.append(_create_metadata_structure_start_scan)
+
+
+    #scan_info_dir=f"/sf/slab/data/{config['pgroup']}/res/scan_info",
+namespace.append_obj(
+    "Scans",
+    data_base_dir="scan_data",
+    #scan_info_dir="/sf/slab/config/eco/test_acq/scan_info",
+    scan_info_dir=f"/sf/slab/data/{config.pgroup()}/res/scan_info",
+    default_counters=[daq],
+    checker=False,
+    scan_directories=True,
+    callbacks_start_scan=callbacks_start_scan,
+    callbacks_end_scan=callbacks_end_scan,
+    run_table=run_table,
+    elog=elog,
+    name="scans",
+    module_name="eco.acquisition.scan",
+    lazy=True,
+)
+
+

eco/utilities/runtable.py

@@ -38,6 +38,7 @@ class Gsheet_API:
         keydf_fname,
         cred_fname,
         exp_id,
+        folder_id,
         exp_path,
         gsheet_key_path,
     ):
@@ -47,7 +48,7 @@ class Gsheet_API:
             "https://www.googleapis.com/auth/drive",
         ]
         self._credentials = ServiceAccountCredentials.from_json_keyfile_name(
-            "/sf/bernina/config/src/python/gspread/pandas_push", self._scope
+            cred_fname, self._scope
         )
         self.gc = gspread.authorize(self._credentials)
         self._keydf_fname = keydf_fname
@@ -60,12 +61,15 @@ class Gsheet_API:
             name="gsheet_keys",
             default_value="metadata thc gps xrd att att_usd kb",
         )
+        self.folder_id = folder_id
         self.init_runtable(exp_id)
 
-    def create_rt_spreadsheet(self, exp_id):
+    def create_rt_spreadsheet(self, exp_id, folder_id=None):
+        if folder_id is None:
+            folder_id = self.folder_id
         self.gc = gspread.authorize(self._credentials)
         spreadsheet = self.gc.create(
-            title=f"run_table_{exp_id}", folder_id="1F7DgF0HW1O71nETpfrTvQ35lRZCs5GvH"
+            title=f"run_table_{exp_id}", folder_id=folder_id
         )
         spreadsheet.add_worksheet("runtable", 10, 10)
         spreadsheet.add_worksheet("positions", 10, 10)
@@ -85,6 +89,8 @@ class Gsheet_API:
     def init_runtable(self, exp_id):
         if os.path.exists(self._keydf_fname):
             self._key_df = pd.read_pickle(self._keydf_fname)
+        else:
+            self._key_df = pd.DataFrame()
         if self._key_df is not None and str(exp_id) in self._key_df.index:
             spreadsheet_key = self._key_df["keys"][f"{exp_id}"]
         else:
@@ -270,8 +276,9 @@ class Run_Table2:
     def __init__(
         self,
         data=None,
-        exp_id="no_exp_id",
-        exp_path="runtable",
+        exp_id='no_exp_id',
+        folder_id = None,
+        exp_path='runtable',
         keydf_fname=None,
         cred_fname=None,
         devices=None,
@@ -285,12 +292,13 @@ class Run_Table2:
             exp_path=exp_path,
             devices=devices,
             name=name,
-        )
+            )
         if np.all([k is not None for k in [keydf_fname, cred_fname, gsheet_key_path]]):
             self._google_sheet_api = Gsheet_API(
                 keydf_fname,
                 cred_fname,
                 exp_id,
+                folder_id,
                 exp_path,
                 gsheet_key_path,
             )
@@ -463,6 +471,8 @@ class Run_Table_DataFrame(DataFrame):
             data_dir.chmod(0o775)
             print(f"Tried to change permissions to 775")
         pd.DataFrame(self).to_pickle(self.fname + "tmp")
+        fp = Path(self.fname + "tmp") 
+        fp.chmod(0o775)
         call(["mv", self.fname + "tmp", self.fname])
 
     def load(self):