queso-cluster 0.0.0__tar.gz

queso_cluster-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: queso-cluster
+Version: 0.0.0
+Summary: Quantifying the Evolution of Spectra with Optimization
+Home-page: https://queso.sriley.dev
+Author: Sarah Olivia Riley
+Author-email: Sarah Riley <sarah.riley1@montana.edu>
+Maintainer-email: Sarah Riley <sarah.riley1@montana.edu>
+Project-URL: Homepage, https://queso.sriley.dev
+Project-URL: Documentation, https://queso.sriley.dev
+Project-URL: Repository, https://github.com/SharkSorceress/queso-cluster
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.25
+Requires-Dist: dkist
+Requires-Dist: scipy
+Requires-Dist: numba
+Requires-Dist: astropy
+Requires-Dist: numba_progress
+Requires-Dist: dask
+Requires-Dist: pyyaml
+Requires-Dist: tol-colors
+Requires-Dist: pint
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+
+# Quantifying the Evolution of Spectra with Optimization (QuESO)
+**Author:** Sarah Olivia Riley (Montana State University)
+ 

queso_cluster-0.0.0/README.md

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+# Quantifying the Evolution of Spectra with Optimization (QuESO)
+**Author:** Sarah Olivia Riley (Montana State University)
+ 

queso_cluster-0.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+
+[project]
+name = "queso-cluster"
+version = "0.0.0"
+authors = [
+	{name = "Sarah Riley", email="sarah.riley1@montana.edu"}
+]
+
+maintainers = [
+	{name = "Sarah Riley", email="sarah.riley1@montana.edu"}
+]
+
+description = "Quantifying the Evolution of Spectra with Optimization"
+readme = "README.md"
+requires-python=">=3.9"
+
+dependencies = [
+	"numpy>=1.25",
+	"dkist",
+	"scipy",
+	"numba",
+	"astropy",
+	"numba_progress",
+	"dask",
+	"pyyaml",
+	"tol-colors",
+	"pint"
+]
+
+classifiers = [
+	# How mature is this project? Common values are
+	#	1 - Planning
+	#	2 - Pre-Alpha
+	#   3 - Alpha
+	#   4 - Beta
+	#   5 - Production/Stable
+	"Development Status :: 2 - Pre-Alpha",
+	"Intended Audience :: Science/Research",
+	"Natural Language :: English",
+	"Programming Language :: Python :: 3.11",
+	"Topic :: Scientific/Engineering :: Astronomy",
+]
+
+[project.urls]
+Homepage = "https://queso.sriley.dev"
+Documentation = "https://queso.sriley.dev"
+Repository = "https://github.com/SharkSorceress/queso-cluster"

queso_cluster-0.0.0/queso_cluster/addon/aia.py

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+#> file:  ./QuESO/addon/aia
+#> lang:  python
+#> synopsis: 
+#> author:   <>
+
+from scipy.io import readsav
+import numpy as np
+
+from .logg import loggTimer
+
+
+@loggTimer
+def delayAIA(fname, epochDev):
+#> detail: 
+#> param type fname:
+#> param type epochDev:
+#> return (type): 
+#> test-method:
+	
+	eD = epochDev
+	print(eD.shape)
+	print(fname)
+	jq_delayCube = readsav(fname)
+
+	#jq_delayCube['arr'][0] --> background of pixel
+	#jq_delayCube['arr'][1] --> background noise of pixel (standard deviation)
+	#jq_delayCube['arr'][2] --> AIA brightness at ViSP slit time
+	#jq_delayCube['arr'][3] --> time of the ViSP slit
+	#jq_delayCube['arr'][4] --> xpos
+	#jq_delayCube['arr'][5] --> ypos
+	#jq_delayCube['arr'][6] --> brightness of peak (before ViSP time)
+	#jq_delayCube['arr'][7] --> time of peak before ViSP time
+	#jq_delayCube['arr'][8] --> brightness of peak (after ViSP time)
+	#jq_delayCube['arr'][9] --> time of peak after ViSP time
+
+
+	jq_AIAFrame = np.zeros((514, 295)) + np.nan
+	#momentFrame = np.zeros(len(jq_delayCube['arr'][:, 4])) + np.nan
+
+	#moment_compare = eD.dataSquare[:, eD.spectralWindow[0]:eD.spectralWindow[1]].mean(axis=-1).reshape(eD.shape[0], eD.shape[1])
+
+	#aia_correct =  lambda x: x.reshape((295, 514)).T.reshape(514*295)
+	correct = lambda x: x.reshape(eD.shape[1], eD.shape[0]).T.reshape(eD.shape[0]*eD.shape[1])
+
+	jq_AIAMask 	= np.zeros(jq_AIAFrame.shape) + np.nan
+	jq_indxMap 	= np.zeros(jq_AIAFrame.shape) + np.nan
+	jq_AIABright = np.zeros(jq_AIAFrame.shape) + np.nan
+
+	#print([0.01937, eD.deltas['pxlAlongSlit']])
+	#print([0.21420, eD.deltas['pxlSlitWidth']])
+
+	dy = 0.01937
+	dx = 0.214167
+
+
+	for i in range(len(jq_delayCube['arr'][:, 4])):
+		xx = int(np.floor(jq_delayCube['arr'][int(i), 4]*dx*6))
+		yy = int(np.floor(jq_delayCube['arr'][int(i), 5]*dy*6))
+
+		if jq_delayCube['arr'][i, 7] > 0:
+			jq_AIAFrame[xx, yy] = jq_delayCube['arr'][i, 3] - jq_delayCube['arr'][i, 7] 
+			jq_AIAMask[xx, yy] = 1
+
+			jq_AIABright[xx, yy] = jq_delayCube['arr'][i, 2]
+		if jq_delayCube['arr'][i, 9] > 0:
+			jq_AIAFrame[xx, yy] = jq_delayCube['arr'][i, 3] - jq_delayCube['arr'][i, 9]
+			jq_AIAMask[xx, yy] = 1
+
+			jq_AIABright[xx, yy] = jq_delayCube['arr'][i, 2]
+
+		jq_indxMap[xx, yy] = i
+
+
+	visp_jqDelayFrame 	= np.zeros(eD.dataSquare.shape[0]) + np.nan
+	visp_jqMaskFrame 	= np.zeros(eD.dataSquare.shape[0]) + np.nan
+	visp_aiaIndx 		= np.zeros(eD.dataSquare.shape[0]) + np.nan
+	visp_aiaBright 		= np.zeros(eD.dataSquare.shape[0]) + np.nan
+	for i in range(eD.dataSquare.shape[0]):
+		yy = int(np.floor((i / eD.shape[0])*dy*6))
+		xx = int(np.floor(np.mod(i, eD.shape[0])*dx*6))
+
+		if ~(np.isnan(jq_AIAMask[xx, yy])):
+			visp_jqMaskFrame[i] 	= jq_AIAMask[xx, yy]
+			visp_aiaIndx[i] 		= jq_indxMap[xx, yy]
+			visp_aiaBright[i] 		= jq_AIABright[xx, yy]
+			visp_jqDelayFrame[i] 	= jq_AIAFrame[xx, yy]
+
+	delayCube 	= correct(visp_jqDelayFrame)/60.#)/60.
+	aiaATvisp  	= correct(visp_aiaBright)
+	aiaIndxMap 	= correct(visp_aiaIndx)
+
+	mask_map = np.zeros(delayCube.shape)
+	mask_map[np.where(~np.isnan(delayCube))] = 1
+
+	import matplotlib.pyplot as plt
+	fig = plt.figure(layout='constrained', figsize=(10, 5), dpi=300)
+	ax = fig.add_subplot(111)
+
+	ax.imshow(mask_map.reshape(eD.shape[0], eD.shape[1]).T, cmap='Greys_r', origin='lower', extent=[0, eD.shape[0]*dx, 0, eD.shape[1]*dy])
+	fig.savefig("./maskTest.png")
+	plt.close()
+
+	return(delayCube, aiaATvisp, aiaIndxMap, mask_map.astype(bool))

queso_cluster-0.0.0/queso_cluster/addon/logg.py

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+#> file:  ./QuESO/addon/logg
+#> lang:  python
+#> synopsis: 
+#> author:   <>
+import logging
+import timeit 
+
+logger = logging.getLogger("queso_cluster")
+logger.addHandler(logging.NullHandler())
+
+def loggTimer(func):
+#> detail: 
+#> param type func:
+#> return (type): 
+#> test-method:
+	def wrapper(*args, **kwargs):
+		__log__ = logg("start", val="{}".format(func.__name__))
+		value = func(*args, **kwargs)
+		logg("stop", _log=__log__)
+		return(value)
+	return(wrapper)
+
+
+def logg(tag, val=None, _time=None, _log=None):
+#> detail: 
+#> param type tag:
+#> param type [None] val:
+#> param type [None] _time:
+#> param type [None] _log:
+#> return (type): 
+#> test-method:
+	ptag = '[' + tag.upper() + '\t]'
+	if _log is not None:
+		val, _time = _log
+	if _time is not None:
+		dur = timeit.default_timer() - _time
+	match tag:
+		case 'aloha': 
+			if _log is not None:
+				log_str = ptag + '[' + duration_string(dur) + ']'
+			else:
+				#print(ptag + 'DURATION\tMESSAGES\tRUNNERS')
+				logger.info(ptag)
+				return(None, timeit.default_timer())
+		case 'start': 
+			log_str = ptag + '\t\t' + val.upper()
+			logger.info(log_str)
+			return(val.upper(), timeit.default_timer())
+		case 'stop': 
+			log_str = ptag + '[' + duration_string(dur) + ']\t' + val.upper()
+		case 'msg': 
+			log_str = ptag + '\t\t' + val.upper()
+		case 'warn':
+			logger.warning(val.upper())
+			return None
+		case 'error':
+			logger.error(val.upper())
+			return None
+	logger.info(log_str)
+
+def duration_string(dur):
+#> detail: 
+#> param type dur:
+#> return (type): 
+#> test-method:
+	return("{:02d}h {:02d}m {:02d}s".format(int(dur/3600), int(int(dur/60) % 60), int(dur % 60))) 

queso_cluster-0.0.0/queso_cluster/addon/multiline.py

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+#> file:  ./QuESO/addon/multiline
+#> lang:  python
+#> synopsis: 
+#> author:   <>
+

queso_cluster-0.0.0/queso_cluster/addon/prep.py

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+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+
+from . import style as sty
+def figureBackup01(analysisObj, dataSquare=None):
+    ii, jj = analysisObj.spectralWindow
+    if dataSquare is None:
+        dataSquare = analysisObj.dataSquare
+    
+    moment0_integrated = dataSquare[:, ii:jj+1].mean(axis=-1).compute()
+    print(moment0_integrated.shape)
+    moment0_continuum = dataSquare[:, analysisObj.continuum].compute()
+    print(moment0_continuum.shape)
+
+    i0_layerCount = len(analysisObj.clusterConfig['intrinsic'])
+
+    fig = plt.figure(layout='constrained', figsize=(5*i0_layerCount, 5), dpi=300)
+
+    moment0 = {'window': moment0_integrated, 'continuum': moment0_continuum}
+    binWidth = {'window': 0.01, 'continuum': 0.01}
+
+    for i in range(i0_layerCount):
+        label = analysisObj.config.clusterConfig['intrinsic'][i]['label']
+        bins  = analysisObj.config.clusterConfig['intrinsic'][i]['layerConfig']['bins']
+
+        ax = fig.add_subplot(1, i0_layerCount, i+1)
+        histBins = np.arange(0, np.ceil(np.nanmax(moment0[label])*10)/10, step=binWidth[label])
+        ax.hist(moment0[label], bins=histBins, range=histBins, rwidth=1, fill=False, histtype='step', color='black')
+        _, color_pallet =  sty._genColorPallet(len(np.diff(bins)))
+
+        for j in range(len(bins)-2):
+            ax.axvline(x = bins[j+1] , color=mpl.colors.rgb2hex(color_pallet[j+1]))
+
+
+    return(fig)