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Fix: revised depth logic to handle custom depths #255

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Fix: revised depth logic to handle custom depths #255

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d50e61e
refactor depth logic to include top depth (#251)
jjmaynard Jun 9, 2025
2db57c7
fix: add top depth to json output (#251)
jjmaynard Jun 9, 2025
f2b189a
fix: lint-format
jjmaynard Jun 9, 2025
a59c9ba
fix: update test_us.py depth logic to handle custom depths
jjmaynard Jun 16, 2025
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9 changes: 6 additions & 3 deletions soil_id/tests/us/test_us.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@
def test_soil_location():
# Dummy Soil Profile Data (replicating the structure provided)
soilHorizon = ["LOAM"] * 7
horizonDepth = [1, 10, 20, 50, 70, 100, 120]
topDepth = [0, 1, 10, 20, 50, 70, 100]
bottomDepth = [1, 10, 20, 50, 70, 100, 120]
rfvDepth = ["0-1%"] * 7
lab_Color = [[41.24, 2.54, 21.17]] * 7
bedrock = None
Expand All @@ -59,7 +60,8 @@ def test_soil_location():
item["lat"],
list_soils_result,
soilHorizon,
horizonDepth,
topDepth,
bottomDepth,
rfvDepth,
lab_Color,
pSlope,
Expand All @@ -76,7 +78,8 @@ def test_empty_rank():
test_locations[0]["lat"],
SoilListOutputData,
soilHorizon=[],
horizonDepth=[],
topDepth=[],
bottomDepth=[],
rfvDepth=[],
lab_Color=[],
pSlope=None,
Expand Down
56 changes: 30 additions & 26 deletions soil_id/us_soil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -276,7 +276,8 @@ def list_soils(lon, lat):
snd_lyrs = []
cly_lyrs = []
txt_lyrs = []
hz_lyrs = []
hzt_lyrs = []
hzb_lyrs = []
rf_lyrs = []
cec_lyrs = []
ph_lyrs = []
Expand Down Expand Up @@ -329,6 +330,7 @@ def list_soils(lon, lat):
OSD_rfv_int.append("No")

# extract horizon data
hz_dept = group_sorted["hzdept_r"]
hz_depb = group_sorted["hzdepb_r"]
snd_d = group_sorted["sandtotal_r"]
cly_d = group_sorted["claytotal_r"]
Expand All @@ -338,6 +340,7 @@ def list_soils(lon, lat):
ec_d = group_sorted["EC"]
ph_d = group_sorted["pH"]

hz_dept = hz_dept.fillna("")
hz_depb = hz_depb.fillna("")
snd_d = snd_d.fillna("")
cly_d = cly_d.fillna("")
Expand All @@ -353,7 +356,8 @@ def list_soils(lon, lat):
cec_lyrs.append(dict(zip(cec_d.index, cec_d)))
ph_lyrs.append(dict(zip(ph_d.index, ph_d)))
ec_lyrs.append(dict(zip(ec_d.index, ec_d)))
hz_lyrs.append(dict(zip(hz_depb.index, hz_depb)))
hzt_lyrs.append(dict(zip(hz_dept.index, hz_dept)))
hzb_lyrs.append(dict(zip(hz_depb.index, hz_depb)))

cokey_group = group_sorted["cokey"].iloc[0]
compname_group = group_sorted["compname"].iloc[0]
Expand Down Expand Up @@ -933,8 +937,8 @@ def list_soils(lon, lat):
# empty string
for lyr in [cec_lyrs, ph_lyrs, ec_lyrs]:
if len(lyr[index]) == 1 and lyr[index][0] == "":
empty_values = [""] * len(hz_lyrs[index])
lyr[index] = dict(zip(hz_lyrs[index], empty_values))
empty_values = [""] * len(hzb_lyrs[index])
lyr[index] = dict(zip(hzb_lyrs[index], empty_values))

else:
OSDhorzdata_group_cokey[index] = group_sorted
Expand All @@ -948,12 +952,12 @@ def list_soils(lon, lat):
lab_intpl_lyrs.append(lab_intpl)

# Create dummy data for lab_lyrs
lab_dummy = [["", "", ""] for _ in range(len(hz_lyrs[index]))]
lab_lyrs.append(dict(zip(hz_lyrs[index].keys(), lab_dummy)))
lab_dummy = [["", "", ""] for _ in range(len(hzb_lyrs[index]))]
lab_lyrs.append(dict(zip(hzb_lyrs[index].keys(), lab_dummy)))

# Create dummy data for munsell_lyrs
munsell_dummy = [""] * len(hz_lyrs[index])
munsell_lyrs.append(dict(zip(hz_lyrs[index].keys(), munsell_dummy)))
munsell_dummy = [""] * len(hzb_lyrs[index])
munsell_lyrs.append(dict(zip(hzb_lyrs[index].keys(), munsell_dummy)))

# Series URL Generation
# Initialize lists to store series URLs
Expand Down Expand Up @@ -1001,7 +1005,7 @@ def list_soils(lon, lat):
lab_intpl_lyrs.append(lab_intpl)

# Create dummy data for lab and munsell layers
keys = list(hz_lyrs[i].keys())
keys = list(hzb_lyrs[i].keys())
lab_dummy = [{"", "", ""} for _ in range(len(keys))]
munsell_dummy = [""] * len(keys)

Expand Down Expand Up @@ -1032,7 +1036,7 @@ def list_soils(lon, lat):
lab_intpl_lyrs.append(lab_intpl)

# Create dummy data for lab and munsell layers
keys = list(hz_lyrs[i].keys())
keys = list(hzb_lyrs[i].keys())
lab_dummy = [{"", "", ""} for _ in range(len(keys))]
munsell_dummy = [""] * len(keys)

Expand Down Expand Up @@ -1078,7 +1082,8 @@ def list_soils(lon, lat):
cec_lyrs,
ph_lyrs,
ec_lyrs,
hz_lyrs,
hzt_lyrs,
hzb_lyrs,
lab_lyrs,
munsell_lyrs,
]
Expand All @@ -1098,7 +1103,8 @@ def list_soils(lon, lat):
cec_lyrs,
ph_lyrs,
ec_lyrs,
hz_lyrs,
hzt_lyrs,
hzb_lyrs,
lab_lyrs,
munsell_lyrs,
) = layer_lists
Expand Down Expand Up @@ -1433,7 +1439,8 @@ def list_soils(lon, lat):
# Reordering lists using list comprehension and mucomp_index
lists_to_reorder = [
esd_comp_list,
hz_lyrs,
hzt_lyrs,
hzb_lyrs,
snd_lyrs,
cly_lyrs,
txt_lyrs,
Expand All @@ -1449,7 +1456,8 @@ def list_soils(lon, lat):
# Destructuring reordered lists for clarity
(
esd_comp_list,
hz_lyrs,
hzt_lyrs,
hzb_lyrs,
snd_lyrs,
cly_lyrs,
txt_lyrs,
Expand All @@ -1469,6 +1477,7 @@ def list_soils(lon, lat):
"id",
"site",
"esd",
"top_depth",
"bottom_depth",
"sand",
"clay",
Expand All @@ -1487,7 +1496,8 @@ def list_soils(lon, lat):
ID,
Site,
esd_comp_list,
hz_lyrs,
hzt_lyrs,
hzb_lyrs,
snd_lyrs,
cly_lyrs,
txt_lyrs,
Expand Down Expand Up @@ -1534,7 +1544,8 @@ def rank_soils(
lat,
list_output_data: SoilListOutputData,
soilHorizon,
horizonDepth,
topDepth,
bottomDepth,
rfvDepth,
lab_Color,
pSlope,
Expand All @@ -1553,7 +1564,8 @@ def rank_soils(
soil_df = pd.DataFrame(
{
"soilHorizon": soilHorizon,
"horizonDepth": horizonDepth,
"top": topDepth,
"bottom": bottomDepth,
"rfvDepth": rfvDepth,
"lab_Color": lab_Color,
}
Expand All @@ -1562,15 +1574,9 @@ def rank_soils(
# Drop rows where all values are NaN
soil_df.dropna(how="all", inplace=True)

# Set the bottom of each horizon
soil_df["bottom"] = soil_df["horizonDepth"]

# Replace NaNs with None for consistency
# soil_df.fillna(value=None, inplace=True)

# Calculate the top depth for each horizon
soil_df["top"] = [0] + soil_df["horizonDepth"].iloc[:-1].tolist()

# Adjust the bottom depth based on bedrock depth
if bedrock is not None:
if bedrock is not soil_df.empty and soil_df["bottom"].iloc[-1] > bedrock:
Expand All @@ -1581,9 +1587,6 @@ def rank_soils(
# Set the bottom depth of the last row to the bedrock depth
soil_df.at[last_valid_index, "bottom"] = bedrock

# Drop the original horizonDepth column
soil_df.drop(columns=["horizonDepth"], inplace=True)

# Filter out rows without valid horizon data
relevant_columns = ["soilHorizon", "rfvDepth", "lab_Color"]
soil_df_slice = soil_df.dropna(how="all", subset=relevant_columns)
Expand Down Expand Up @@ -1825,6 +1828,7 @@ def rank_soils(
.drop(["compname"], axis=1)
.columns.tolist()
)

sliceT = sliceT[sample_pedon_slice_vars]

D = gower_distances(sliceT) # Equal weighting given to all soil variables
Expand Down