diff --git a/pozo/renderers/plotly.py b/pozo/renderers/plotly.py index 34146aa1..2fc39897 100644 --- a/pozo/renderers/plotly.py +++ b/pozo/renderers/plotly.py @@ -639,7 +639,7 @@ def get_traces(self, graph, yaxis='y1', xstart=1, **kwargs): fillcolor) # we will lock both axes completely but it seems like mutual zoom operations are ok # notes above on how to do that - if themes['intervals'] == 'category': + if False: pass else: all_traces.append(go.Scatter( diff --git a/pozo/renderers/tree_table.py b/pozo/renderers/tree_table.py index 2c243535..03701bac 100644 --- a/pozo/renderers/tree_table.py +++ b/pozo/renderers/tree_table.py @@ -1,5 +1,5 @@ import pozo.renderers as pzr -from IPython.core.display import HTML, display, Javascript +from IPython.display import HTML, display, Javascript import html def javascript(): diff --git a/pozo/tracks.py b/pozo/tracks.py index 61cc2ec1..3d6f181d 100644 --- a/pozo/tracks.py +++ b/pozo/tracks.py @@ -2,16 +2,17 @@ import pozo import pozo.themes as pzt -class Track(ood.Item, pzt.Themeable): +class Track(ood.Item, pzt.Themeable): def set_name(self, name): return super().set_name(name) def get_name(self): return super().get_name() - _type="track" - _child_type="axis" + _type = "track" + _child_type = "axis" + def __init__(self, *args, **kwargs): super().__init__(**kwargs) self.note_dict = {} @@ -26,7 +27,9 @@ def _check_types(self, *axes): if isinstance(axis, (list)): raw_return.extend(self._check_types(*axis)) elif not isinstance(axis, accepted_types): - raise TypeError(f"Axis.add_axes() only accepts axes, and traces: pozo objects, not {type(axis)}") + raise TypeError( + f"Axis.add_axes() only accepts axes, and traces: pozo objects, not {type(axis)}" + ) elif isinstance(axis, pozo.Trace): raw_return.append(pozo.Axis(axis, name=axis.get_name())) else: @@ -34,12 +37,14 @@ def _check_types(self, *axes): return raw_return def replace_axes(self, *axes, **kwargs): - mnemonics = [] - for axis in axes: - for trace in axis.get_traces(): - mnemonics.append(trace.get_mnemonic()) - self.pop_axes(*mnemonics, strict_index=False, exclude=kwargs.get('exclude', None)) - self.add_axes(*axes, **kwargs) + mnemonics = [] + for axis in axes: + for trace in axis.get_traces(): + mnemonics.append(trace.get_mnemonic()) + self.pop_axes( + *mnemonics, strict_index=False, exclude=kwargs.get("exclude", None) + ) + self.add_axes(*axes, **kwargs) # add_items def add_axes(self, *axes, **kwargs): @@ -84,11 +89,13 @@ def get_traces(self, *selectors, **kwargs): def get_trace(self, selector=0, **kwargs): ret = self.get_traces(selector, **kwargs) - if len(ret) == 0: return None + if len(ret) == 0: + return None return ret[0] def get_theme(self): - context = { "type":"track", - "name": self._name, - } + context = { + "type": "track", + "name": self._name, + } return self._get_theme(context=context) diff --git a/pozo/units/__init__.py b/pozo/units/__init__.py index c38c912b..71ee884d 100644 --- a/pozo/units/__init__.py +++ b/pozo/units/__init__.py @@ -5,63 +5,24 @@ from io import StringIO import pandas as pd -from .units import MissingRangeError, LasMapEntry -from .units import LasRegistry, UnitException, MissingLasUnitWarning -import re +from .registry_config import registry_defines, registry_mapping +from .units import ( + MissingRangeError, + UnitException, + MissingLasUnitWarning, + LasRegistry, +) +import re registry = LasRegistry() -Quantity = Q = registry.Quantity # Overriding the registry and all this is a little weird - -registry.define('gamma_API_unit = [Gamma_Ray_Tool_Response] = gAPI') -registry.define("porosity_unit = percent = pu") -registry.define("of_1 = 100 * percent = fraction") -registry.define("legacy_api_porosity_unit = [Legacy_API_Porosity_Unit] = puAPI") - -PU = [ - LasMapEntry((-50, 80), "pu", "decide by range - MEDIUM"), - LasMapEntry((-.5, .8), "of_1", "decide by range - MEDIUM"), - LasMapEntry((), "puAPI", "catch all, legacy unit - LOW"), - ] -percent_general = [ - LasMapEntry((-100, 100), "percent", "decide by range, verify - LOW"), - LasMapEntry((-1, 1), "of_1", "decide by range, verify - LOW"), - LasMapEntry((), "ppm", "catch all, ppm - LOW" ), - ] - -registry.add_las_map('-', 'MM' , 'millimeter' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'M' , 'meter' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'CM' , 'centimeter' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'GAPI', 'gAPI' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'DEG_C', 'celsius' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'DEG_F', 'fahrenheit' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'COUNTS/S', 'cps' , "decided without mnemonic- MEDIUM") -registry.add_las_map('-', 'CPS', 'cps' , "decided without mnemonic- MEDIUM") -registry.add_las_map('DEPT', 'M' , 'meter' , "HIGH") -registry.add_las_map('DEPT', 'FT' , 'feet' , "HIGH") -registry.add_las_map('DEPT', 'F' , 'feet' , "HIGH") -registry.add_las_map('GR' , 'GAPI', 'gAPI' , "HIGH") -registry.add_las_map('GR' , '', 'gAPI' , "HIGH") -registry.add_las_map('CGR' , 'GAPI', 'gAPI' , "HIGH") -registry.add_las_map('CALI', 'CM' , 'centimeter' , "HIGH") -registry.add_las_map('CALI', 'IN' , 'inch' , "HIGH") -registry.add_las_map('DRHO', 'G/C3', 'gram / centimeter ** 3' , "HIGH") -registry.add_las_map('RHOB', 'G/C3', 'gram / centimeter ** 3' , "HIGH") -registry.add_las_map('DT' , 'US/F', 'microsecond / foot' , "HIGH") -registry.add_las_map('ILD' , 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('LLS' , 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('ILM' , 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('LLD' , 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('SFL' , 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('SGR' , 'GAPI', 'gAPI' , "HIGH") -registry.add_las_map('SP' , 'MV' , 'millivolt' , "HIGH") -registry.add_las_map('MSFL', 'OHMM', 'ohm * meter' , "HIGH") -registry.add_las_map('NPHI', 'PU' , PU) -registry.add_las_map('NPHI', 'PU%' , 'pu' , "HIGH") -registry.add_las_map('PEF' , '' , percent_general) -registry.add_las_map('POTA', '' , percent_general) -registry.add_las_map('THOR', '' , percent_general) -registry.add_las_map('URAN', '' , percent_general) +Quantity = Q = ( + registry.Quantity +) # Overriding the registry and all this is a little weird + +registry_defines(registry) +registry_mapping(registry) + # TODO: Beginning of a database, has to go online # mnemonics, synonyms (resolve- matching in theme, @@ -71,13 +32,15 @@ # versioning, searching # also want it to point to posts -desc_wo_num = re.compile(r'^(?:\s*\d+\s+)?(.*)$') -red_low = re.compile(r'(.+)?(?:LOW|NONE)(.+)?') -orange_medium = re.compile(r'(.+)?MEDIUM(.+)?') +desc_wo_num = re.compile(r"^(?:\s*\d+\s+)?(.*)$") +red_low = re.compile(r"(.+)?(?:LOW|NONE)(.+)?") +orange_medium = re.compile(r"(.+)?MEDIUM(.+)?") + def check_las(las, registry=registry, HTML_out=True, divid=""): - def n0(s): # If None, convert to "" + def n0(s): # If None, convert to "" return "" if s is None else str(s) + # using the warnings like this kind sucks # they do need to be surpressed becuase i'm building a better view into the warnings anyway # with this function, but that resolved = on 87 w/ 91 = on 91 is really weird. @@ -86,57 +49,90 @@ def n0(s): # If None, convert to "" with warnings.catch_warnings(): warnings.simplefilter("default") warnings.filterwarnings("error", category=MissingLasUnitWarning) + d = chr(0X1e) # delimiter - col_names = f"mnemonic{d}las unit{d}pozo mapping{d}confidence{d}parsed{d}description{d}min{d}med{d}max{d}#NaN" - result = [col_names] if HTML_out else [] + col_names = [ + "mnemonic", "las unit", "pozo mapping", "confidence", + "parsed", "description", "min", "med", "max", "#NaN" + ] + result = [f"{d}".join(col_names)] if HTML_out else [] for curve in las.curves: resolved = None pozo_match = None confidence = None parsed = None try: - resolved = registry.resolve_las_unit(curve.mnemonic, curve.unit, curve.data) + resolved = registry.resolve_las_unit( + curve.mnemonic, curve.unit, curve.data + ) if resolved is not None: pozo_match = resolved.unit confidence = resolved.confidence - parsed = registry.parse_unit_from_context(curve.mnemonic, curve.unit, curve.data) - if resolved is None: raise MissingLasUnitWarning("Parsed directly from LAS, probably wrong") - except (pint.UndefinedUnitError, MissingRangeError, UnitException, MissingLasUnitWarning) as e: - confidence = " - " + str(e) + " - NONE" + parsed = registry.parse_unit_from_context( + curve.mnemonic, curve.unit, curve.data + ) + if resolved is None: + raise MissingLasUnitWarning( + "Parsed directly from LAS, probably wrong" + ) + except ( + pint.UndefinedUnitError, + MissingRangeError, + UnitException, + MissingLasUnitWarning, + ) as e: + confidence = f" - {str(e)} - NONE" + find_desc = desc_wo_num.findall(curve.descr) desc = find_desc[0] if len(find_desc) > 0 else curve.descr - [v_min, v_med, v_max] = [str(x) for x in np.nanquantile(curve.data, [0, .5, 1])] + + v_min, v_med, v_max = map(str, np.nanquantile(curve.data, [0, 0.5, 1])) + n_nan = np.count_nonzero(np.isnan(curve.data)) + curve_data = dict( - mnemonic = curve.mnemonic, - las_unit = curve.unit, - pozo_match = pozo_match, - confidence = confidence, - parsed_unit = parsed, - desc = desc, - v_min = v_min, - v_med = v_med, - v_max = v_max, - n_nan = np.count_nonzero(np.isnan(curve.data))) - if not HTML_out: result.append(curve_data) - else: result.append(d.join([n0(x) for x in curve_data.values()])) - if not HTML_out: return result + mnemonic=curve.mnemonic, + las_unit=curve.unit, + pozo_match=pozo_match, + confidence=confidence, + parsed_unit=parsed, + desc=desc, + v_min=v_min, + v_med=v_med, + v_max=v_max, + n_nan=n_nan, + ) + if not HTML_out: + result.append(curve_data) + else: + result.append(d.join([n0(x) for x in curve_data.values()])) + + if not HTML_out: + return result + try: post_result = "\n".join(result) - output = pd.read_csv(StringIO(post_result), delimiter=d, na_filter=False).to_html() + output = pd.read_csv( + StringIO(post_result), delimiter=d, na_filter=False + ).to_html() + for match in red_low.finditer(output): current_match = match.group() - colored = "" + current_match[4:] + colored = '' + current_match[4:] output = output.replace(current_match, colored) + for match in orange_medium.finditer(output): current_match = match.group() - colored = "" + current_match[4:] + colored = '' + current_match[4:] output = output.replace(current_match, colored) - display(HTML('
'+output+'
')) + + display(HTML(f'
{output}
')) + except Exception as e: display(str(e)) display(HTML("
".join(result))) -# Just a shorcut to make the API nice + +# Just a shortcut to make the API nice def parse_unit_from_curve(curve, registry=registry): try: return registry.parse_unit_from_context(curve.mnemonic, curve.unit, curve.data) diff --git a/pozo/units/errors.py b/pozo/units/errors.py new file mode 100644 index 00000000..ee294b2a --- /dev/null +++ b/pozo/units/errors.py @@ -0,0 +1,16 @@ +class MissingLasUnitWarning(UserWarning): + """Warning for unresolved LAS units.""" + + pass + + +class UnitException(Exception): + """Raised when unit parsing fails.""" + + pass + + +class MissingRangeError(Exception): + """Raised when no matching range is found for LAS data.""" + + pass diff --git a/pozo/units/registry_config.py b/pozo/units/registry_config.py new file mode 100644 index 00000000..e178bee2 --- /dev/null +++ b/pozo/units/registry_config.py @@ -0,0 +1,56 @@ +from .units import LasMapEntry + + +PU = [ + LasMapEntry((-50, 80), "pu", "decide by range - MEDIUM"), + LasMapEntry((-0.5, 0.8), "of_1", "decide by range - MEDIUM"), + LasMapEntry((), "puAPI", "catch all, legacy unit - LOW"), +] +percent_general = [ + LasMapEntry((-100, 100), "percent", "decide by range, verify - LOW"), + LasMapEntry((-1, 1), "of_1", "decide by range, verify - LOW"), + LasMapEntry((), "ppm", "catch all, ppm - LOW"), +] + + +def registry_defines(registry): + registry.define("gamma_API_unit = [Gamma_Ray_Tool_Response] = gAPI") + registry.define("porosity_unit = percent = pu") + registry.define("of_1 = 100 * percent = fraction") + registry.define("legacy_api_porosity_unit = [Legacy_API_Porosity_Unit] = puAPI") + + +def registry_mapping(registry): + registry.add_las_map("-", "MM", "millimeter", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "M", "meter", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "CM", "centimeter", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "GAPI", "gAPI", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "DEG_C", "celsius", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "DEG_F", "fahrenheit", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "COUNTS/S", "cps", "decided without mnemonic- MEDIUM") + registry.add_las_map("-", "CPS", "cps", "decided without mnemonic- MEDIUM") + registry.add_las_map("DEPT", "M", "meter", "HIGH") + registry.add_las_map("DEPT", "FT", "feet", "HIGH") + registry.add_las_map("DEPT", "F", "feet", "HIGH") + registry.add_las_map("GR", "GAPI", "gAPI", "HIGH") + registry.add_las_map("GR", "", "gAPI", "HIGH") + registry.add_las_map("CGR", "GAPI", "gAPI", "HIGH") + registry.add_las_map("CALI", "CM", "centimeter", "HIGH") + registry.add_las_map("CALI", "IN", "inch", "HIGH") + registry.add_las_map("DRHO", "G/C3", "gram / centimeter ** 3", "HIGH") + registry.add_las_map("RHOB", "G/C3", "gram / centimeter ** 3", "HIGH") + registry.add_las_map("DT", "US/F", "microsecond / foot", "HIGH") + registry.add_las_map("ILD", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("LLS", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("ILM", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("LLD", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("SFL", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("SGR", "GAPI", "gAPI", "HIGH") + registry.add_las_map("SP", "MV", "millivolt", "HIGH") + registry.add_las_map("MSFL", "OHMM", "ohm * meter", "HIGH") + registry.add_las_map("NPHI", "PU", PU) + registry.add_las_map("NPHI", "PU%", "pu", "HIGH") + registry.add_las_map("PEF", "", percent_general) + registry.add_las_map("POTA", "", percent_general) + registry.add_las_map("THOR", "", percent_general) + registry.add_las_map("URAN", "", percent_general) diff --git a/pozo/units/units.py b/pozo/units/units.py index 4f849cd3..003251e5 100644 --- a/pozo/units/units.py +++ b/pozo/units/units.py @@ -2,37 +2,36 @@ import warnings import numpy as np +import pint # noqa + import pozo -os.environ['PINT_ARRAY_PROTOCOL_FALLBACK'] = "0" # from numpy/pint documentation -import pint # noqa +from .errors import MissingLasUnitWarning, MissingRangeError, UnitException -class MissingLasUnitWarning(UserWarning): - pass +os.environ["PINT_ARRAY_PROTOCOL_FALLBACK"] = "0" # from numpy/pint documentation -class UnitException(Exception): - pass -class MissingRangeError(Exception): - pass +class LasMapEntry: + def __init__(self, boundaries, unit, confidence): + if not isinstance(boundaries, tuple) or len(boundaries) not in {0, 2}: + raise TypeError( + "add_las_map ranges should contain a tuple with (min, max) or () catch-all" + ) -class LasMapEntry(): - def __init__(self, boundries, unit, confidence): - if not isinstance(boundries, tuple) or not (len(boundries) == 0 or len(boundries) == 2): - raise TypeError("add_las_map ranges should contain a tuple with (min, max) or () catch-all") - self.boundries = boundries + self.boundaries = boundaries self.unit = unit self.confidence = confidence def check(self, min_val, max_val): - if len(self.boundries) == 0: + if len(self.boundaries) == 0: return True - elif min_val > self.boundries[0] and max_val < self.boundries[1]: + elif min_val > self.boundaries[0] and max_val < self.boundaries[1]: return True return False + # Namespace would be nicer and I could hide registries if this wasn't overriden # But would the map be global? -# Or would we just use a default registery like in init +# Or would we just use a default register like in init class LasRegistry(pint.UnitRegistry): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @@ -41,31 +40,44 @@ def __init__(self, *args, **kwargs): def add_las_map(self, mnemonic, unit, ranges, confidence="- not indicated - LOW"): if not isinstance(ranges, list): - if not isinstance(ranges, LasMapEntry): - ranges = [LasMapEntry((), ranges, confidence)] - else: - ranges = [ranges] + ranges = ( + [LasMapEntry((), ranges, confidence)] + if not isinstance(ranges, LasMapEntry) + else [ranges] + ) + for ra in ranges: if not isinstance(ra, LasMapEntry): - raise TypeError("Improperly formated map for LasMap, should be type LasMapEntry") - self.parse_units(ra.unit) # Can't check in LasMapEntry because don't have registry + raise TypeError( + "Improperly formated map for LasMap, should be type LasMapEntry" + ) + # Can't check in LasMapEntry because don't have registry + self.parse_units(ra.unit) + if mnemonic not in self._mnemonic_units: self._mnemonic_units[mnemonic] = {} self._reverse_mnemonic_units[mnemonic] = {} + self._mnemonic_units[mnemonic][unit] = ranges + for ra in ranges: - self._reverse_mnemonic_units[mnemonic][self.parse_units(ra.unit)] = unit # doesn't this override + self._reverse_mnemonic_units[mnemonic][self.parse_units(ra.unit)] = ( + unit # doesn't this override + ) def resolve_SI_unit_to_las(self, mnemonic, unit): unit = unit if isinstance(unit, pint.Unit) else self.parse_units(unit) # TODO: looking up the dimension would be nice mnemonic = pozo.deLASio(mnemonic) - if mnemonic in self._reverse_mnemonic_units and unit in self._reverse_mnemonic_units[mnemonic]: + if ( + mnemonic in self._reverse_mnemonic_units + and unit in self._reverse_mnemonic_units[mnemonic] + ): return self._reverse_mnemonic_units[mnemonic][unit] elif unit in self._reverse_mnemonic_units["-"]: return self._reverse_mnemonic_units["-"][unit] - else: return None - + else: + return None def resolve_las_unit(self, mnemonic, unit, data): mnemonic = pozo.deLASio(mnemonic) @@ -81,10 +93,13 @@ def resolve_las_unit(self, mnemonic, unit, data): for ra in ranges: if ra.check(min_val, max_val): return ra - raise MissingRangeError(f"{unit} for {mnemonic} found but not in range: {ranges}.") + raise MissingRangeError( + f"{unit} for {mnemonic} found but not in range: {ranges}." + ) return None - def parse_unit_from_context(self, mnemonic, unit, data): # this just gives you a result + # this just gives you a result + def parse_unit_from_context(self, mnemonic, unit, data): resolved = None try: resolved = self.resolve_las_unit(mnemonic, unit, data) @@ -98,14 +113,17 @@ def parse_unit_from_context(self, mnemonic, unit, data): # this just gives you a return None else: try: - if not unit or unit == "": raise UnitException("Empty unit not allowed- please map it") + if not unit or unit == "": + raise UnitException("Empty unit not allowed- please map it") try: return self.parse_units(unit) except Exception as e: warnings.warn(f"Couldn't parse unit: {e}", MissingLasUnitWarning) return None except pint.UndefinedUnitError as e: - raise UnitException(f"'{unit}' for '{pozo.deLASio(mnemonic)}' not found.") from e + raise UnitException( + f"'{unit}' for '{pozo.deLASio(mnemonic)}' not found." + ) from e -# we now don't get confidence from string +# we now don't get confidence from string diff --git a/pyproject.toml b/pyproject.toml index 6e2d746f..d146239d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,8 +22,9 @@ dependencies = [ 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