keep add convenient records for data file paths and propagate through scripts...

keep add convenient records for data file paths and propagate through scripts and top-level imports; also adjust for file IO adjustments for sequences

absorption_imaging.py

@@ -2,10 +2,7 @@ from lib import *
 from lib import CONNECTIONS as C
 import datetime, sys, pathlib
 
-outdir = (
-    pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data\absorption imaging")
-        .joinpath(str(datetime.datetime.now()).replace(':', '').split('.')[0])
-)
+outdir = DATADIRS.absorption_imaging.joinpath(get_timestamp())
 
 comments = """
 62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil, keep MOT beams on
@@ -14,7 +11,7 @@ comments = """
 # BUILD SEQUENCE
 t0 = 10.0 # turn off the MOT
 t1 = t0 + 1.0e-3 # start imaging sequence
-SEQ = SuperSequence({
+SEQ = SuperSequence(outdir, "sequence", {
     "Sequence": (Sequence
         .digital_hilo(*C.dummy, 0.0, t0 + 0.2)
         .with_color("k").with_stack_idx(0)
@@ -93,7 +90,7 @@ class AbsorptionImaging(Controller):
 
     def run_sequence(self, *args):
         self.comp.run()
-        SEQ.save(outdir)
+        SEQ.save()
 
     def run_camera(self, *args):
         frames = self.cam.acquire_frames(3)

atom_trajectory.py

@@ -2,10 +2,7 @@ from lib import *
 from lib import CONNECTIONS as C
 import datetime, sys, pathlib
 
-outdir = (
-    pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data\fluorescence imaging")
-        .joinpath(str(datetime.datetime.now()).replace(':', '').split('.')[0])
-)
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
 
 comments = """
 62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil
@@ -21,7 +18,7 @@ seq_camera = Sequence()
 for tau in T_camera:
     seq_camera += Sequence.digital_pulse(*C.camera, t0 + tau, 1000.0e-6)
 
-SEQ = SuperSequence({
+SEQ = SuperSequence(outdir, "sequence", {
     "Sequence": (Sequence
         .digital_hilo(*C.dummy, 0.0, t0 + T_camera.max() + 100e-3)
         .with_color("k").with_stack_idx(0)
@@ -79,7 +76,7 @@ class AtomTrajectory(Controller):
 
     def run_sequence(self, *args):
         self.comp.run()
-        SEQ.save(outdir)
+        SEQ.save()
 
     def run_camera(self, *args):
         frames = self.cam.acquire_frames(len(T_camera))

fluorescence_imaging.py

@@ -2,10 +2,7 @@ from lib import *
 from lib import CONNECTIONS as C
 import datetime, sys, pathlib
 
-outdir = (
-    pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data\fluorescence imaging")
-        .joinpath(str(datetime.datetime.now()).replace(':', '').split('.')[0])
-)
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
 
 comments = """
 62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil
@@ -24,7 +21,7 @@ camera_config = {
 # BUILD SEQUENCE
 t0 = 10.0 # turn off the push beam
 
-SEQ = SuperSequence({
+SEQ = SuperSequence(outdir, "sequence", {
     "Sequence": (Sequence
         .digital_hilo(*C.dummy, 0.0, t0 + 100e-3)
         .with_color("k").with_stack_idx(0)
@@ -75,7 +72,7 @@ class FluorescenceImaging(Controller):
 
     def run_sequence(self, *args):
         self.comp.run()
-        SEQ.save(outdir)
+        SEQ.save()
 
     def run_camera(self, *args):
         frames = self.cam.acquire_frames(1)

lib/__init__.py

@@ -21,7 +21,15 @@ from lib.control import (
     Controller,
 )
 from lib.system import (
+    DATADIRS,
     MAIN,
     CONNECTIONS,
     FLIR,
 )
+from lib.dataio import (
+    get_timestamp,
+    fresh_filename,
+    DataPaths,
+    gen_table_fmt,
+    print_write,
+)

lib/dataio.py

+import datetime
+import pathlib
+
+def gen_table_fmt(label_fmts, s="  ", L=12, P=5, K=2) -> (str, str):
+    """
+    Generate the column labels and format string of a table from a list of
+    tuples following
+        (
+            'column label',
+            x in {'s','s>','i','f','g','e'},
+            {l: length override, p: precision override} (optional)
+        )
+    """
+    head = ""
+    lines = ""
+    fmt = ""
+    names = list()
+    for label_fmt in label_fmts:
+        names.append(label_fmt[0])
+        overrides = dict() if len(label_fmt) < 3 else label_fmt[2]
+        l = overrides.get("l",
+            max(int((len(label_fmt[0])+K-1)/K)*K, L*(label_fmt[1] in ['e','f','g']))
+        )
+        p = overrides.get("p",
+            l-7 if (l-7 >= 1 and l-7 <= P) else P
+        )
+        head += "{:"+str(l)+"s}"+s
+        lines += l*"-" + s
+        if label_fmt[1] == 's':
+            fmt += "{:"+str(l)+"s}"+s
+        elif label_fmt[1] == 's>':
+            fmt += "{:>"+str(l)+"s}"+s
+        elif label_fmt[1] == 'i':
+            fmt += "{:"+str(l)+".0f}"+s
+        elif label_fmt[1] in ['e', 'f', 'g']:
+            fmt += "{:"+str(l)+"."+str(p)+label_fmt[1]+"}"+s
+        else:
+            raise Exception("Format is not one of {'s', 's>', 'i', 'f', 'g', 'e'}")
+    head = head[:-len(s)]
+    lines = lines[:-len(s)]
+    fmt = fmt[:-len(s)]
+    return head.format(*names)+"\n"+lines, fmt
+
+def print_write(outfile, s, end="\n", flush=True) -> None:
+    print(s, end=end, flush=flush)
+    outfile.write(s+end)
+    if flush:
+        outfile.flush()
+    return None
+
+def get_timestamp():
+    return format(datetime.datetime.now(), "%Y-%m-%d_%H%M%S")
+
+class DataPaths:
+    def __init__(self, **paths: dict[str, pathlib.Path]):
+        self.paths = paths
+
+    def __getattr__(self, attr):
+        return self.paths[attr]
+
+def fresh_filename(path: pathlib.Path, overwrite: bool=False) -> pathlib.Path:
+    if overwrite:
+        return path
+    _path = path
+    while _path.is_file():
+        print(f"WARNING: found existinf file {_path}")
+        _path = _path.with_stem(_path.stem + "_")
+        print(f"Write instead to {_path}")
+    return _path
+

lib/imaging.py

@@ -11,27 +11,18 @@ import toml
 import warnings
 import PIL.Image
 import lib.plotdefs as pd
+import lib.dataio as io
 
 H = 6.626070040e-34
 C = 2.99792458e+8
 
 DEF_DX = 3.45 # pixel size for Flir Grasshopper [um]
 
-def _fresh_filename(path: pathlib.Path, overwrite: bool=False) -> pathlib.Path:
-    if overwrite:
-        return path
-    _path = path
-    while _path.is_file():
-        print(f"WARNING: found existinf file {_path}")
-        _path = _path.with_stem(_path.stem + "_")
-        print(f"Write instead to {_path}")
-    return _path
-
 class ImagingData:
-    def __init__(self, name: str, arrays: dict[str, np.ndarray],
+    def __init__(self, outdir: pathlib.Path, arrays: dict[str, np.ndarray],
             config: dict[str, ...], comments: str=None,
             results: dict[str, ...]=None):
-        self.name = name
+        self.outdir = outdir
         self.arrays = arrays
         self.config = config
         self.comments = str() if comments is None else comments
@@ -39,27 +30,27 @@ class ImagingData:
 
     def save(self, target: pathlib.Path=None, overwrite: bool=False,
             printflag: bool=True):
-        T = pathlib.Path(self.name) if target is None else target
-        if printflag: print(f"[imaging] Saving data to {T}:")
+        T = self.outdir if target is None else target
+        if printflag: print(f"[imaging] Saving data to '{T}':")
         if not T.is_dir():
             if printflag: print(f"[imaging] mkdir {T}")
             T.mkdir(parents=True, exist_ok=True)
 
-        arrays_file = _fresh_filename(T.joinpath("arrays.npz"), overwrite)
+        arrays_file = io.fresh_filename(T.joinpath("arrays.npz"), overwrite)
         if printflag: print("[imaging] save arrays")
         np.savez_compressed(arrays_file, **self.arrays)
 
-        config_file = _fresh_filename(T.joinpath("config.toml"), overwrite)
+        config_file = io.fresh_filename(T.joinpath("config.toml"), overwrite)
         if printflag: print("[imaging] save camera config")
         with config_file.open('w') as outfile:
             toml.dump(self.config, outfile)
 
-        comments_file = _fresh_filename(T.joinpath("comments.txt"), overwrite)
+        comments_file = io.fresh_filename(T.joinpath("comments.txt"), overwrite)
         if printflag: print("[imaging] save comments")
         comments_file.write_text(self.comments)
 
         if self.results is not None:
-            results_file = _fresh_filename(
+            results_file = io.fresh_filename(
                 T.joinpath("results.toml"), overwrite)
             if printflag: print("[imaging] save results")
             with results_file.open('w') as outfile:
@@ -68,22 +59,23 @@ class ImagingData:
         return self
 
     @staticmethod
-    def load(target: pathlib.Path, name: str=None, printflag: bool=True):
-        name = target.stem if name is None else name
-        if printflag: print(f"[imaging] Loading data from {target}:")
+    def load(target: pathlib.Path, outdir: pathlib.Path=None,
+            printflag: bool=True):
+        outdir = target if outdir is None else target
+        if printflag: print(f"[imaging] Loading data from target '{target}':")
         if not target.is_dir():
-            raise Exception(f"Target {target} does not exist")
+            raise Exception(f"Target '{target}' does not exist")
 
         arrays_file = target.joinpath("arrays.npz")
         if printflag: print("[imaging] load arrays")
         if not arrays_file.is_file():
-            raise Exception(f"Arrays file {arrays_file} does not exist")
+            raise Exception(f"Arrays file '{arrays_file}' does not exist")
         arrays = np.load(arrays_file)
 
         config_file = target.joinpath("config.toml")
         if printflag: print("[imaging] load camera config")
         if not config_file.is_file():
-            raise Exception(f"Config file {config_file} does not exist")
+            raise Exception(f"Config file '{config_file}' does not exist")
         config = toml.load(config_file)
 
         comments_file = target.joinpath("comments.txt")
@@ -96,11 +88,11 @@ class ImagingData:
         results = results_file.read_text() \
                 if results_file.is_file() else None
         #if printflag: print("  Done.")
-        return AbsorptionData(name, arrays, config, comments, results)
+        return AbsorptionData(outdir, arrays, config, comments, results)
 
     def render_arrays(self, target: pathlib.Path=None, dx=None,
             printflag: bool=True):
-        T = pathlib.Path(self.name) if target is None else target
+        T = self.outdir if target is None else target
         T = T.joinpath("images")
         _dx = self.config.get("bin_size", 1) * (DEF_DX if dx is None else dx)
         if printflag: print(f"[imaging] Render images to {T}:")
@@ -108,7 +100,7 @@ class ImagingData:
             if printflag: print(f"[imaging] mkdir {T}")
             T.mkdir(parents=True, exist_ok=True)
         for label, array in self.arrays.items():
-            if printflag: print(f"[imaging] render {label}")
+            if printflag: print(f"[imaging] render '{label}'")
             if label == "od":
                 warnings.filterwarnings("ignore")
                 H, W = array.shape

lib/system.py

@@ -6,9 +6,19 @@ from lib.ew import (
     AnalogConnection as Analog,
 )
 from lib.flir import Grasshopper
+from lib.dataio import DataPaths
+import pathlib
+
+DATA_HOME = pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data")
+DATADIRS = DataPaths(
+    home                    = DATA_HOME,
+    absorption_imaging      = DATA_HOME.joinpath("absorption imaging"),
+    fluorescence_imaging    = DATA_HOME.joinpath("fluorescence imaging"),
+)
 
 CONNECTIONS = ConnectionLayout(
     coils       = Digital(0,  2, 1),
+    coil_cur    = Analog(1,  4.01),
     shims       = Digital(0,  0, 0),
     mot_laser   = Digital(1,  7, 1),
     push        = Digital(0,  3, 1),

loading_rate.py

@@ -2,10 +2,7 @@ from lib import *
 from lib import CONNECTIONS as C
 import datetime, sys, pathlib
 
-outdir = (
-    pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data\fluorescence imaging")
-        .joinpath(str(datetime.datetime.now()).replace(':', '').split('.')[0])
-)
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
 
 comments = """
 62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil
@@ -26,7 +23,7 @@ t0 = 5.0 # take a picure at t0
 DT = np.linspace(0.0, 2.5, 50)
 
 def make_sequence(dt):
-    SEQ = SuperSequence({
+    SEQ = SuperSequence(outdir.joinpath("sequences"), f"dt_{dt:.5f}", {
         "Sequence": (Sequence
             .digital_hilo(*C.dummy, 0.0, t0 + 100e-3)
             .with_color("k").with_stack_idx(0)
@@ -89,6 +86,7 @@ class LoadingRate(Controller):
                 .run()
                 .clear()
             )
+            SEQ.save()
 
     def run_camera(self, *args):
         frames = self.cam.acquire_frames(len(DT))
@@ -103,7 +101,8 @@ class LoadingRate(Controller):
         data.render_arrays()
 
     def cmd_visualize(self, *args):
-        SEQ.draw_simple().show().close()
+        make_sequence(float(args[0]) if len(args) > 0 else DT.max()) \
+                .draw_simple().show().close()
         sys.exit(0)
 
 if __name__ == "__main__":

mot_survival.py

@@ -2,10 +2,7 @@ from lib import *
 from lib import CONNECTIONS as C
 import datetime, sys, pathlib
 
-outdir = (
-    pathlib.Path(r"C:\Users\EW\University of Illinois - Urbana\Covey Lab - Documents\Data\fluorescence imaging")
-        .joinpath(str(datetime.datetime.now()).replace(':', '').split('.')[0])
-)
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
 
 comments = """
 62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil
@@ -26,7 +23,7 @@ t0 = 5.0 # let the MOT sit for t0 seconds
 DT = np.append(np.array([0]), np.linspace(3e-3, 50e-3, 20))
 
 def make_sequence(dt):
-    SEQ = SuperSequence({
+    SEQ = SuperSequence(outdir.joinpath("sequences"), f"dt_{dt:.5f}", {
         "Sequence": (Sequence
             .digital_hilo(*C.dummy, 0.0, t0 + DT.max() + 100e-3)
             .with_color("k").with_stack_idx(0)
@@ -97,7 +94,8 @@ class MOTSurvival(Controller):
         data.render_arrays()
 
     def cmd_visualize(self, *args):
-        SEQ.draw_simple().show().close()
+        make_sequence(float(args[0]) if len(args) > 0 else DT.max()) \
+                .draw_simple().show().close()
         sys.exit(0)
 
 if __name__ == "__main__":