Commit b026df97 authored by BO ZHANG's avatar BO ZHANG 🏀
Browse files

major updates

parent cad9fd06

.gitignore

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unit_test_data_root

.idea/*

*.png

*.DS_Store*

Makefile

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@@ -12,6 +12,6 @@ uninstall: 
	pip uninstall $(PKG) -y



test:

	coverage run -m  pytest . --import-mode=importlib --cov-report=html --cov-report=term-missing

	coverage run -m  pytest . --cov=$(PKG) --import-mode=importlib --cov-report=html --cov-report=term-missing

	coverage report -m

	rm -rf .coverage .pytest_cache

README.md

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@@ -44,42 +44,3 @@ from csst_common.params import CSST_PARAMS as CP 
print(CP)

print(CP["mbi"]["detector2filter"])

```
 


how to use data_manager

```python

from csst_common.data_manager import CsstMbiDataManager

dm = CsstMbiDataManager(...)

# access L0 directory

dm.dir_l0

# access L1 directory

dm.dir_l1

# access dir_pcref

dm.dir_pcref

# access path_aux

dm.path_aux

# access ver_sim

dm.ver_sim

# access target detectors

dm.target_detectors

# access available detectors

dm.available_detectors

# define an L1 file (detector-specified)

dm.l1_detector(detector=6)

# define an L1 file (non-detector-specified)

dm.l1_file("flipped_image.fits")

```



a shortcut for test dataset



```python

from csst_common.data_manager import CsstMbiDataManager



CsstMbiDataManager.quickstart(ver_sim="C5.2", dir_l1=".", exposure_id=100)

```



## algorithm description



The `csst_common` provides some common modules for CSST pipeline.



- `csst_common.parameters`

- `csst_common.data_manager`

csst_common/__init__.py

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@@ -9,10 +9,10 @@ Modified-History: 
    2022-09-13, Bo Zhang, fixed a bug

"""



import os



from .status import CsstResult, CsstStatus

from .pipeline import Pipeline

from .ccds import CCDS

from .dfs import DFS

from .decorator import parameterized_module_decorator



__version__ = "0.0.1"



PACKAGE_PATH = os.path.dirname(__file__)
 
__version__ = "0.0.2"

csst_common/ccds/slsconf.py

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import json

import os

import re



import astropy.io.fits as pyfits



from ccds import client





# chipid: [01,   02,   03,   04,   05,   10,   21,   26,   27,   28,   29,   30]

# filter: [GI,   GV,   GU,   GU,   GV,   GI,   GI,   GV,   GU,   GU,   GV,   GI]

# clabel: [GI-1, GV-1, GU-1, GU-2, GV-2, GI-2, GI-3, GV-3, GU-3, GU-4, GV-4, GI-4]





def get_version():

    observatory = client.get_default_observatory()

    operational_context = client.get_default_context(observatory)

    ver = re.split(r"[_.]", operational_context)[1]

    return ver





def resave_sensitivity(dir_save, chipid, flt):

    ver = get_version()

    h = pyfits.open(

        dir_save + "CSST_MSC_MS_SENSITIVITY_" + chipid + "_" + ver + ".fits"

    )

    for extname, order in zip(

        ["L0ST", "LP1ST", "LM1ST", "LP2ST", "LM2ST"],

        ["0st", "1st", "-1st", "2st", "-2st"],

    ):

        hdu0 = pyfits.PrimaryHDU()

        hdu1 = pyfits.BinTableHDU(h[extname].data)

        hdul = pyfits.HDUList([hdu0, hdu1])

        hdul.writeto(

            dir_save + "CSST_MSC_MS_SENSITIVITY_" + flt + "_" + order + ".fits",

            overwrite=True,

            checksum=True,

        )





def readjson(dir_save, fjsoname):

    with open(dir_save + fjsoname) as f:

        d = json.load(f)

    return d





##################################################################################

##################################################################################



# keys = ['BEAMA', 'MMAG_EXTRACT_A', 'MMAG_MARK_A', 'DYDX_ORDER_A', 'DYDX_A_0', 'DYDX_A_1', 'XOFF_A', 'YOFF_A',

#         'DISP_ORDER_A', 'DLDP_A_0', 'DLDP_A_1', 'BEAMB', 'MMAG_EXTRACT_B', 'MMAG_MARK_B', 'DYDX_ORDER_B', 'DYDX_B_0',

#         'XOFF_B', 'YOFF_B', 'DISP_ORDER_B', 'DLDP_B_0', 'DLDP_B_1', 'BEAMC', 'MMAG_EXTRACT_C', 'MMAG_MARK_C',

#         'DYDX_ORDER_C', 'DYDX_C_0', 'DYDX_C_1', 'XOFF_C', 'YOFF_C', 'DISP_ORDER_C', 'DLDP_C_0', 'DLDP_C_1', 'BEAMD',

#         'MMAG_EXTRACT_D', 'MMAG_MARK_D', 'DYDX_ORDER_D', 'DYDX_D_0', 'DYDX_D_1', 'XOFF_D', 'YOFF_D', 'DISP_ORDER_D',

#         'DLDP_D_0', 'DLDP_D_1', 'BEAME', 'MMAG_EXTRACT_E', 'MMAG_MARK_E', 'DYDX_ORDER_E', 'DYDX_E_0', 'DYDX_E_1',

#         'XOFF_E', 'YOFF_E', 'DISP_ORDER_E', 'DLDP_E_0', 'DLDP_E_1']



GL = [

    "GI2",

    "GV4",

    "GU2",

    "GU4",

    "GV2",

    "GI4",

    "GI6",

    "GV8",

    "GU6",

    "GU8",

    "GV6",

    "GI8",

]

GR = [

    "GI1",

    "GV3",

    "GU1",

    "GU3",

    "GV1",

    "GI3",

    "GI5",

    "GV7",

    "GU5",

    "GU7",

    "GV5",

    "GI7",

]

SEN = ["GI", "GV", "GU", "GU", "GV", "GI", "GI", "GV", "GU", "GU", "GV", "GI"]





def fwriteKEY(fsx, i):

    fsx.write("INSTRUMENT CSSTSLS" + "\n")

    fsx.write("CAMERA " + SEN[i] + "\n")

    if SEN[i] == "GI":

        fsx.write("WAVELENGTH 6200 10000" + "\n")

    elif SEN[i] == "GV":

        fsx.write("WAVELENGTH 4000 6200" + "\n")

    elif SEN[i] == "GU":

        fsx.write("WAVELENGTH 2550 4000" + "\n")

    fsx.write("\n" + "SCIENCE_EXT SCI ; Science extension" + "\n")

    fsx.write("DQ_EXT DQ       ; DQ extension" + "\n")

    fsx.write("ERRORS_EXT ERR  ; Error extension" + "\n")

    fsx.write("FFNAME csstFlat.fits" + "\n")

    fsx.write("DQMASK 246    ; 4096 and 512 taken out" + "\n")

    fsx.write("\n" + "RDNOISE 5.0" + "\n")

    fsx.write("EXPTIME EXPTIME" + "\n")

    fsx.write("POBJSIZE 1.0" + "\n")

    fsx.write("#SMFACTOR 1.0" + "\n\n")





def fwriteBEAM(

    dir_save,

    fsx,

    i,

    GRATINGLR,

    BEAMX,

    MMAG_EXTRACT_X,

    MMAG_MARK_X,

    DYDX_ORDER_X,

    DYDX_X_0,

    DYDX_X_1,

    XOFF_X,

    YOFF_X,

    DISP_ORDER_X,

    DLDP_X_0,

    DLDP_X_1,

):

    ver = get_version()

    [

        d01_GI21,

        d02_GV43,

        d03_GU21,

        d04_GU43,

        d05_GV21,

        d10_GI43,

        d21_GI65,

        d26_GV87,

        d27_GU65,

        d28_GU87,

        d29_GV65,

        d30_GI87,

    ] = [

        readjson(dir_save, "CSST_MSC_MS_EXTRACT1D_" + chipid + "_" + ver + ".json")

        for chipid in [

            "01",

            "02",

            "03",

            "04",

            "05",

            "10",

            "21",

            "26",

            "27",

            "28",

            "29",

            "30",

        ]

    ]

    d = [

        d01_GI21,

        d02_GV43,

        d03_GU21,

        d04_GU43,

        d05_GV21,

        d10_GI43,

        d21_GI65,

        d26_GV87,

        d27_GU65,

        d28_GU87,

        d29_GV65,

        d30_GI87,

    ]

    fsx.write(BEAMX), [

        fsx.write(" " + str(d[i][GRATINGLR][BEAMX][j]))

        for j in range(len(d[i][GRATINGLR][BEAMX]))

    ], fsx.write("\n")

    fsx.write(MMAG_EXTRACT_X + " " + str(d[i][GRATINGLR][MMAG_EXTRACT_X]) + "\n")

    fsx.write(MMAG_MARK_X + " " + str(d[i][GRATINGLR][MMAG_MARK_X]) + "\n")

    fsx.write("# " + "\n")

    fsx.write("# Trace description " + "\n")

    fsx.write("# " + "\n")

    fsx.write(DYDX_ORDER_X + " " + str(d[i][GRATINGLR][DYDX_ORDER_X]) + "\n")

    fsx.write(DYDX_X_0), [

        fsx.write(" " + str(d[i][GRATINGLR][DYDX_X_0][j]))

        for j in range(len(d[i][GRATINGLR][DYDX_X_0]))

    ], fsx.write("\n")

    if BEAMX == "BEAMB":

        pass

    else:

        fsx.write(DYDX_X_1), [

            fsx.write(" " + str(d[i][GRATINGLR][DYDX_X_1][j]))

            for j in range(len(d[i][GRATINGLR][DYDX_X_1]))

        ], fsx.write("\n")

    fsx.write("# " + "\n")

    fsx.write("# X and Y Offsets " + "\n")

    fsx.write("# " + "\n")

    fsx.write(XOFF_X + " " + str(d[i][GRATINGLR][XOFF_X]) + "\n")

    fsx.write(YOFF_X + " " + str(d[i][GRATINGLR][YOFF_X]) + "\n")

    fsx.write("# " + "\n")

    fsx.write("# Dispersion solution " + "\n")

    fsx.write("# " + "\n")

    fsx.write(DISP_ORDER_X + " " + str(d[i][GRATINGLR][DISP_ORDER_X]) + "\n")

    fsx.write(DLDP_X_0), [

        fsx.write(" " + str(d[i][GRATINGLR][DLDP_X_0][j]))

        for j in range(len(d[i][GRATINGLR][DLDP_X_0]))

    ], fsx.write("\n")

    fsx.write(DLDP_X_1), [

        fsx.write(" " + str(d[i][GRATINGLR][DLDP_X_1][j]))

        for j in range(len(d[i][GRATINGLR][DLDP_X_1]))

    ], fsx.write("\n")

    fsx.write("# " + "\n")

    if BEAMX == "BEAMA":

        ordername = "1st"

        fsx.write(

            "SENSITIVITY_A CSST_MSC_MS_SENSITIVITY_" + SEN[i] + "_1st.fits" + "\n"

        )

    elif BEAMX == "BEAMB":

        ordername = "0st"

        fsx.write(

            "SENSITIVITY_B CSST_MSC_MS_SENSITIVITY_" + SEN[i] + "_0st.fits" + "\n"

        )

    elif BEAMX == "BEAMC":

        ordername = "-1st"

        fsx.write(

            "SENSITIVITY_C CSST_MSC_MS_SENSITIVITY_" + SEN[i] + "_-1st.fits" + "\n"

        )

    elif BEAMX == "BEAMD":

        ordername = "2st"

        fsx.write(

            "SENSITIVITY_D CSST_MSC_MS_SENSITIVITY_" + SEN[i] + "_2st.fits" + "\n"

        )

    elif BEAMX == "BEAME":

        ordername = "-2st"

        fsx.write(

            "SENSITIVITY_E CSST_MSC_MS_SENSITIVITY_" + SEN[i] + "_-2st.fits" + "\n"

        )

    fsx.write("# " + "\n" + "\n")





def fsave_conf(dir_save, GLR, GRATINGLR, i):

    c = dir_save + "CSST_MSC_MS_" + GLR[i] + ".conf"

    os.system("> " + c)

    fs = open(c, "a")

    fwriteKEY(fs, i)

    fs.write("# 1 order (BEAM A) *******************" + "\n")

    fwriteBEAM(

        dir_save,

        fs,

        i,

        GRATINGLR,

        "BEAMA",

        "MMAG_EXTRACT_A",

        "MMAG_MARK_A",

        "DYDX_ORDER_A",

        "DYDX_A_0",

        "DYDX_A_1",

        "XOFF_A",

        "YOFF_A",

        "DISP_ORDER_A",

        "DLDP_A_0",

        "DLDP_A_1",

    )

    fs.write("\n# 0 order (BEAM B) *******************" + "\n")

    fwriteBEAM(

        dir_save,

        fs,

        i,

        GRATINGLR,

        "BEAMB",

        "MMAG_EXTRACT_B",

        "MMAG_MARK_B",

        "DYDX_ORDER_B",

        "DYDX_B_0",

        "DYDX_B_1",

        "XOFF_B",

        "YOFF_B",

        "DISP_ORDER_B",

        "DLDP_B_0",

        "DLDP_B_1",

    )

    fs.write("\n# -1 order (BEAM C) *******************" + "\n")

    fwriteBEAM(

        dir_save,

        fs,

        i,

        GRATINGLR,

        "BEAMC",

        "MMAG_EXTRACT_C",

        "MMAG_MARK_C",

        "DYDX_ORDER_C",

        "DYDX_C_0",

        "DYDX_C_1",

        "XOFF_C",

        "YOFF_C",

        "DISP_ORDER_C",

        "DLDP_C_0",

        "DLDP_C_1",

    )

    fs.write("\n# 2 order (BEAM D) *******************" + "\n")

    fwriteBEAM(

        dir_save,

        fs,

        i,

        GRATINGLR,

        "BEAMD",

        "MMAG_EXTRACT_D",

        "MMAG_MARK_D",

        "DYDX_ORDER_D",

        "DYDX_D_0",

        "DYDX_D_1",

        "XOFF_D",

        "YOFF_D",

        "DISP_ORDER_D",

        "DLDP_D_0",

        "DLDP_D_1",

    )

    fs.write("\n# -2 order (BEAM E) *******************" + "\n")

    fwriteBEAM(

        dir_save,

        fs,

        i,

        GRATINGLR,

        "BEAME",

        "MMAG_EXTRACT_E",

        "MMAG_MARK_E",

        "DYDX_ORDER_E",

        "DYDX_E_0",

        "DYDX_E_1",

        "XOFF_E",

        "YOFF_E",

        "DISP_ORDER_E",

        "DLDP_E_0",

        "DLDP_E_1",

    )

    fs.close()





def get_slsconf(dir_save=".", **kwargs):

    """save SLS conf files to `dir_save`"""



    # resave the sensitivity.fits

    for chipid, flt in zip(["01", "02", "03"], ["GI", "GV", "GU"]):

        resave_sensitivity(dir_save, chipid, flt)



    # save CSST_MSC_MS_*.conf

    for i in range(0, 12):

        fsave_conf(dir_save, GL, "GRATINGL", i)

        fsave_conf(dir_save, GR, "GRATINGR", i)



    # TODO: assert all files are saved correctly, then return



    # TODO: return a dict containing filepath mapping