Merge branch 'feat-step4-intg' of https://github.com/brown-ccv/icesat…

…2-tracks into feat-step4-intg

src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py

@@ -1,26 +1,21 @@
-import os, sys
-
-from icesat2_tracks.config.IceSAT2_startup import (
-    mconfig,
-    xr,
-    color_schemes,
-    plt,
-    font_for_print,
-    np,
-)
+import sys
+import datetime
 
 import h5py
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.font_manager as font_for_print
+from matplotlib.gridspec import GridSpec
+import xarray as xr
+from siphon.catalog import TDSCatalog
+
+from icesat2_tracks.config.IceSAT2_startup import mconfig
 import icesat2_tracks.ICEsat2_SI_tools.io as io
 import icesat2_tracks.ICEsat2_SI_tools.wave_tools as waves
 import icesat2_tracks.local_modules.m_tools_ph3 as MT
 import icesat2_tracks.local_modules.m_general_ph3 as M
-
-from siphon.catalog import TDSCatalog
-
-import pandas as pd
-
-import datetime
-from matplotlib.gridspec import GridSpec
+from icesat2_tracks.config.IceSAT2_startup import color_schemes
 
 color_schemes.colormaps2(21)
 
@@ -425,8 +420,6 @@ def test_nan_frac(imask):
 except:
     target_name = "A02_" + track_name + "_hindcast_fail"
 
-
-# %%
 def plot_prior(Prior, axx):
     angle = Prior["incident_angle"][
         "value"

src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py

@@ -1,35 +1,27 @@
-#
 """
 This file open a ICEsat2 tbeam_stats.pyrack applied filters and corections and returns smoothed photon heights on a regular grid in an .nc file.
 This is python 3.11
 """
-import os, sys
+import sys
+import datetime
+import copy
+
+import xarray as xr
+from sliderule import sliderule, icesat2
+
 from icesat2_tracks.config.IceSAT2_startup import (
     mconfig,
-    xr,
     color_schemes,
     font_for_pres,
     plt,
 )
-
-import geopandas as gpd
-
-from sliderule import sliderule, icesat2, earthdata
-
-import shapely
-from ipyleaflet import basemaps, Map, GeoData
-
 import icesat2_tracks.ICEsat2_SI_tools.sliderule_converter_tools as sct
 import icesat2_tracks.ICEsat2_SI_tools.io as io
 import icesat2_tracks.ICEsat2_SI_tools.beam_stats as beam_stats
 import icesat2_tracks.local_modules.m_tools_ph3 as MT
 from icesat2_tracks.local_modules import m_general_ph3 as M
 
 
-import h5py, imp, copy
-import datetime
-
-
 xr.set_options(display_style="text")
 
 
@@ -39,7 +31,6 @@
     sys.argv
 )  # loads standard experiment
 
-# 20190502052058_05180312_005_01
 plot_flag = True
 hemis = batch_key.split("_")[0]
 
@@ -118,8 +109,6 @@
 
 
 # main routine for defining the x coordinate and sacing table data
-
-
 def make_B01_dict(table_data, split_by_beam=True, to_hdf5=False):
     """
     converts a GeoDataFrame from Sliderule to GeoDataFrames for each beam witht the correct columns and names
@@ -166,7 +155,7 @@ def make_B01_dict(table_data, split_by_beam=True, to_hdf5=False):
 
 # define reference point and then define 'x'
 table_data = copy.copy(gdf)
-imp.reload(sct)
+
 # the reference point is defined as the most equatorward point of the polygon.
 # It's distance from the equator is  subtracted from the distance of each photon.
 table_data = sct.define_x_coordinate_from_data(table_data)
@@ -181,7 +170,6 @@ def make_B01_dict(table_data, split_by_beam=True, to_hdf5=False):
     Ti[kk]["heights_c_weighted_mean"] = Ti[kk]["h_mean"].copy()
     Ti[kk]["heights_c_std"] = Ti[kk]["h_sigma"].copy()
 
-
 segment = track_name.split("_")[1][-2:]
 ID_name = sct.create_ID_name(gdf.iloc[0], segment=segment)
 print(ID_name)
@@ -203,7 +191,6 @@ def make_B01_dict(table_data, split_by_beam=True, to_hdf5=False):
 F_atl06.save_light(path=plot_path, name="B01b_ATL06_corrected.png")
 plt.close()
 
-imp.reload(beam_stats)
 if plot_flag:
     font_for_pres()
     F = M.figure_axis_xy(8, 4.3, view_scale=0.6)

src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py

@@ -1,31 +1,27 @@
-import sys
-
-
 """
 This file open a ICEsat2 track applied filters and corections and returns smoothed photon heights on a regular grid in an .nc file.
 This is python 3
 """
 
-from icesat2_tracks.config.IceSAT2_startup import mconfig, xr, plt, np
-
+import copy
+import datetime
+import h5py
+import time
+import sys
 
-from threadpoolctl import threadpool_info, threadpool_limits
+import numpy as np
+import xarray as xr
 from pprint import pprint
+from scipy.ndimage.measurements import label
+from threadpoolctl import threadpool_info, threadpool_limits
 
-
-import h5py
+import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
 import icesat2_tracks.ICEsat2_SI_tools.io as io
 import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec
-
-import time
-import imp
-import copy
-from icesat2_tracks.local_modules.m_spectrum_ph3 import spicke_remover
-import datetime
-import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
-from scipy.ndimage.measurements import label
+import icesat2_tracks.local_modules.m_general_ph3 as M
+import icesat2_tracks.local_modules.m_spectrum_ph3 as spicke_remover
 import icesat2_tracks.local_modules.m_tools_ph3 as MT
-from icesat2_tracks.local_modules import m_general_ph3 as M
+from icesat2_tracks.config.IceSAT2_startup import mconfig, plt
 
 import tracemalloc
 
@@ -99,7 +95,7 @@ def linear_gap_fill(F, key_lead, key_int):
     Ib = Gd[group[1]]
     ratio = Ia["x"][:].size / Ib["x"][:].size
     if (ratio > 10) | (ratio < 0.1):
-        print("bad data ratio ", ratio, 1 / ratio)
+        # print("bad data ratio ", ratio, 1 / ratio) # TODO: add logger
         bad_ratio_flag = True
 
 if (np.array(nan_fraction).mean() > 0.95) | bad_ratio_flag:
@@ -118,7 +114,6 @@ def linear_gap_fill(F, key_lead, key_int):
     exit()
 
 # test LS with an even grid where missing values are set to 0
-imp.reload(spec)
 print(Gd.keys())
 Gi = Gd[list(Gd.keys())[0]]  # to select a test  beam
 dist = io.get_beam_var_hdf_store(Gd[list(Gd.keys())[0]], "dist")
@@ -153,10 +148,10 @@ def linear_gap_fill(F, key_lead, key_int):
 print("define global xlims")
 dist_list = np.array([np.nan, np.nan])
 for k in all_beams:
-    print(k)
+    # print(k) # TODO: add logger
     hkey = "heights_c_weighted_mean"
     x = Gd[k + "/dist"][:]
-    print(x[0], x[-1])
+    # print(x[0], x[-1]) # TODO: add logger
     dist_list = np.vstack([dist_list, [x[0], x[-1]]])
 
 xlims = np.nanmin(dist_list[:, 0]) - dx, np.nanmin(dist_list[:, 1])
@@ -172,7 +167,7 @@ def linear_gap_fill(F, key_lead, key_int):
 for k in all_beams:
     dist_i = io.get_beam_var_hdf_store(Gd[k], "dist")
     x_mask = (dist_i > xlims[0]) & (dist_i < xlims[1])
-    print(k, sum(x_mask["dist"]) / (xlims[1] - xlims[0]))
+    # print(k, sum(x_mask["dist"]) / (xlims[1] - xlims[0])) # TODO: add logger
 
 
 print("-reduced frequency resolution")
@@ -199,7 +194,7 @@ def linear_gap_fill(F, key_lead, key_int):
     Gi = io.get_beam_hdf_store(Gd[k])
     x_mask = (Gi["dist"] > xlims[0]) & (Gi["dist"] < xlims[1])
     if sum(x_mask) / (xlims[1] - xlims[0]) < 0.005:
-        print("------------------- not data in beam found; skip")
+        # print("------------------- not data in beam found; skip") # TODO: add logger
         continue
 
     Gd_cut = Gi[x_mask]
@@ -219,7 +214,7 @@ def linear_gap_fill(F, key_lead, key_int):
 
     # compute slope spectra !!
     dd = np.gradient(dd)
-    dd, _ = spicke_remover(dd, spreed=10, verbose=False)
+    dd, _ = spicke_remover.spicke_remover(dd, spreed=10, verbose=False)
     dd_nans = (np.isnan(dd)) + (Gd_cut["N_photos"] <= 5)
 
     # using gappy data

src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py

@@ -3,45 +3,31 @@
 This is python 3
 """
 import sys
-
-from icesat2_tracks.config.IceSAT2_startup import (
-    mconfig,
-    xr,
-    color_schemes,
-    plt,
-    np,
-    font_for_print,
-)
-
-import icesat2_tracks.ICEsat2_SI_tools.io as io
-import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec
-
-import time
+import numpy as np
+import xarray as xr
 from matplotlib.gridspec import GridSpec
+import icesat2_tracks.ICEsat2_SI_tools.io as io
 import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
-from scipy.ndimage.measurements import label
 import icesat2_tracks.local_modules.m_tools_ph3 as MT
 from icesat2_tracks.local_modules import m_general_ph3 as M
-
+from icesat2_tracks.config.IceSAT2_startup import mconfig, color_schemes, plt, font_for_print
 
 track_name, batch_key, test_flag = io.init_from_input(
-    sys.argv
+    sys.argv # TODO: Handle via CLI
 )  # loads standard experiment
 hemis, batch = batch_key.split("_")
 
 load_path = mconfig["paths"]["work"] + batch_key + "/B02_spectra/"
-load_file = load_path + "B02_" + track_name  # + '.nc'
+load_file = load_path + "B02_" + track_name
 plot_path = (
     mconfig["paths"]["plot"] + "/" + hemis + "/" + batch_key + "/" + track_name + "/"
-)
+) # TODO: Update with pathlib
 MT.mkdirs_r(plot_path)
 
 Gk = xr.open_dataset(load_file + "_gFT_k.nc")
 Gx = xr.open_dataset(load_file + "_gFT_x.nc")
 
 Gfft = xr.open_dataset(load_file + "_FFT.nc")
-time.sleep(2)
-
 
 all_beams = mconfig["beams"]["all_beams"]
 high_beams = mconfig["beams"]["high_beams"]

src/icesat2_tracks/config/IceSAT2_startup.py

@@ -1,26 +1,11 @@
 import os
 import pathlib
-###
-#   THIS FILE IS A LOCAL FILE
-#   it is not maintained via git, it contains configs specific to the machine
-###
+import string
 
-#os.environ["DISPLAY"] = "localhost:10.0"
-# 14, 16,  work
-#standart libraries:
-import numpy as np
-import matplotlib
 import matplotlib.pyplot as plt
 
-import matplotlib.colors as colors
-import pandas as pd
 from icesat2_tracks.local_modules import m_colormanager_ph3 as M_color
 from icesat2_tracks.local_modules import m_tools_ph3 as MT
-from icesat2_tracks.local_modules import m_general_ph3 as M
-
-import string
-
-import xarray as xr
 
 ## Read folders and configuration paths
 config_dir_path = os.path.dirname(__file__)
@@ -37,12 +22,10 @@
 #load colorscheme
 color_schemes=M_color.color(path=mconfig['paths']['config'], name='color_def')
 
-
 lstrings =iter([i+') ' for i in list(string.ascii_lowercase)])
 # define journal fig sizes
 fig_sizes = mconfig['fig_sizes']['AMS']
 
-
 SMALL_SIZE = 8
 MEDIUM_SIZE = 10
 BIGGER_SIZE = 12
@@ -52,11 +35,11 @@
 plt.rc('font', size=SMALL_SIZE, serif='Helvetica Neue', weight='normal')          # controls default text sizes
 plt.rc('text', usetex='false')
 plt.rc('axes', titlesize=MEDIUM_SIZE, labelweight='normal')     # fontsize of the axes title
-plt.rc('axes', labelsize=SMALL_SIZE, labelweight='normal') #, family='bold')    # fontsize of the x and y labels
+plt.rc('axes', labelsize=SMALL_SIZE, labelweight='normal') # fontsize of the x and y labels
 plt.rc('xtick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
 plt.rc('ytick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
 plt.rc('legend', fontsize=SMALL_SIZE, frameon=False)    # legend fontsize
-plt.rc('figure', titlesize=MEDIUM_SIZE, titleweight='bold', autolayout=True) #, family='bold')  # fontsize of the figure title
+plt.rc('figure', titlesize=MEDIUM_SIZE, titleweight='bold', autolayout=True) # fontsize of the figure title
 plt.rc('path', simplify=True)
 plt.rcParams['figure.figsize'] = (10, 8)
 plt.rcParams['pcolor.shading'] = 'auto'
@@ -66,15 +49,7 @@
 plt.rc('axes', labelsize= MEDIUM_SIZE, labelweight='normal')
 plt.rc('axes.spines', top= False, right=False )
 
-
-
-def font_for_print():
-
-    SMALL_SIZE = 6
-    MEDIUM_SIZE = 8
-    BIGGER_SIZE = 10 # not used. CP
-    legend_properties = {'weight':'bold'} # not used. CP
-
+def font_for_print(SMALL_SIZE = 6, MEDIUM_SIZE = 8):
     plt.rc('font', size=SMALL_SIZE, serif='Helvetica Neue', weight='normal')          # controls default text sizes
     plt.rc('text', usetex='false')
     plt.rc('axes', titlesize=MEDIUM_SIZE, labelweight='normal')     # fontsize of the axes title
@@ -85,21 +60,13 @@ def font_for_print():
     plt.rc('figure', titlesize=MEDIUM_SIZE, titleweight='bold', autolayout=True) #, family='bold')  # fontsize of the figure title
     plt.rc('axes', labelsize= SMALL_SIZE, labelweight='normal')
 
-def font_for_pres():
-
-    SMALL_SIZE = 10
-    MEDIUM_SIZE = 12
-    BIGGER_SIZE = 14 # not used. CP
-    legend_properties = {'weight':'bold'} # not used. CP
-
-
-    plt.rc('font', size=SMALL_SIZE, serif='Helvetica Neue', weight='normal')          # controls default text sizes
+def font_for_pres(SMALL_SIZE = 10, MEDIUM_SIZE = 12):
+    plt.rc('font', size=SMALL_SIZE, serif='Helvetica Neue', weight='normal') # controls default text sizes
     plt.rc('text', usetex='false')
     plt.rc('axes', titlesize=MEDIUM_SIZE, labelweight='normal')     # fontsize of the axes title
     plt.rc('axes', labelsize=SMALL_SIZE, labelweight='normal') #, family='bold')    # fontsize of the x and y labels
     plt.rc('xtick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
     plt.rc('ytick', labelsize=SMALL_SIZE)    # fontsize of the tick labels
     plt.rc('legend', fontsize=SMALL_SIZE, frameon=False)    # legend fontsize
-    plt.rc('figure', titlesize=MEDIUM_SIZE, titleweight='bold', autolayout=True) #, family='bold')  # fontsize of the figure title
-
+    plt.rc('figure', titlesize=MEDIUM_SIZE, titleweight='bold', autolayout=True) # fontsize of the figure title
     plt.rc('axes', labelsize= SMALL_SIZE, labelweight='normal')