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wip troubleshoot ingredient_key_dict error
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@rugeli
rugeli committed Jul 22, 2024
1 parent bcab5b4 commit 0ff5204
Showing 1 changed file with 79 additions and 42 deletions.
121 changes: 79 additions & 42 deletions cellpack/autopack/Analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -312,9 +312,6 @@ def run_distance_analysis(
]
)

df = pd.DataFrame()
df["Ingredient key"] = []
df["Pairwise distance distribution"] = []
img_list = []
for ingr_key in all_pairwise_distances:
ingr_distance_histo_path = figure_path.glob(
Expand All @@ -327,11 +324,18 @@ def run_distance_analysis(
path=f"{output_image_location}/{img_path.name}",
)
)
text_list = [
"Ingredient key",
"Pairwise distance distribution",
*[
val
for pair in zip(all_pairwise_distances.keys(), img_list)
for val in pair
],
]

md_object.add_table(header="Pairwise Distance Distributions", table=pd.DataFrame([text_list]))

df = pd.DataFrame()
df["Ingredient key"] = all_pairwise_distances.keys()
df["Pairwise distance distribution"] = img_list
md_object.add_table(header="", table=df)

def get_ingredient_key_from_object_or_comp_name(
self, search_name, ingredient_key_dict
Expand Down Expand Up @@ -409,6 +413,7 @@ def run_partner_analysis(
if len(partner_pair_dict):
md_object.add_header(header="Partner Analysis")

val_list = []
paired_keys = []
touching_radii = []
binding_probabilities = []
Expand All @@ -422,18 +427,38 @@ def run_partner_analysis(
numpy.count_nonzero(pairwise_distances < padded_radius)
/ partner_values["num_packed"]
)
paired_keys.append(paired_key)
touching_radii.append(partner_values["touching_radius"])
binding_probabilities.append(partner_values["binding_probability"])
close_fractions.append(close_fraction)
val_list.extend(
[
paired_key,
partner_values["touching_radius"],
partner_values["binding_probability"],
close_fraction,
]
)

df = pd.DataFrame()
df["Paired keys"] = paired_keys
df["Touching radii"] = touching_radii
df["Binding probabilities"] = binding_probabilities
df["Close packing fractions"] = close_fractions
text_list = [
"Partner pair",
"Touching radius",
"Binding probability",
"Close packed fraction",
*val_list,
]
md_object.add_table(
header="",
text=text_list,
)
# paired_keys.append(paired_key)
# touching_radii.append(partner_values["touching_radius"])
# binding_probabilities.append(partner_values["binding_probability"])
# close_fractions.append(close_fraction)

md_object.add_table(header="", table=df)
# df = pd.DataFrame()
# df["Paired keys"] = paired_keys
# df["Touching radii"] = touching_radii
# df["Binding probabilities"] = binding_probabilities
# df["Close packing fractions"] = close_fractions

# md_object.add_table(header="", table=df)

def create_report(
self,
Expand All @@ -460,7 +485,23 @@ def create_report(
run_*_analysis: bool
whether to run specific analysis
"""
self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_key_*")
if report_output_path is None:
report_output_path = self.output_path
report_output_path = Path(report_output_path)

# initialize MarkdownWriter object
md_object = MarkdownWriter(
title="Packing analysis report",
output_path=self.output_path,
output_image_location=output_image_location,
report_name="analysis_report",
)

md_object.add_header(
header=f"Analysis for packing results located at {self.packing_results_path}", level=2
)
if not hasattr(self, "ingredient_key_dict"):
self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_key_*")

if ingredient_keys is None:
ingredient_keys = list(self.ingredient_key_dict.keys())
Expand All @@ -469,38 +510,33 @@ def create_report(
ingredient_keys=ingredient_keys
)
ingredient_radii = self.get_ingredient_radii(recipe_data=recipe_data)
pairwise_distance_dict = self.read_dict_from_glob_file(
"pairwise_distances_*.json"
)
combined_pairwise_distance_dict = self.combine_results_from_seeds(
pairwise_distance_dict
)


if not hasattr(self, "pairwise_distance_dict"):
self.pairwise_distance_dict = self.read_dict_from_glob_file(
"pairwise_distances_*.json"
)

df = pd.DataFrame()
df["Ingredient name"] = list(ingredient_keys)
df["Encapsulating radius"] = list(ingredient_radii.values())
df["Average number packed"] = list(avg_num_packed.values())

# path to save report and other outputs
if output_image_location is None:
output_image_location = self.output_path

md_object = MarkdownWriter(
title="Packing analysis report",
output_path=self.output_path,
output_image_location=output_image_location,
report_name="analysis_report",
combined_pairwise_distance_dict = self.combine_results_from_seeds(
self.pairwise_distance_dict
)

md_object.add_header(
header=f"Analysis for packing results located at {self.packing_results_path}"
)
val_list = []
for key, radius, num_packed in zip(ingredient_keys, ingredient_radii.values(), avg_num_packed.values()):
val_list.extend([key, radius, num_packed])
text_list = [
"Ingredient name",
"Encapsulating radius",
"Average number packed",
*val_list,
]
# table_data = pd.DataFrame({
# "Ingredient name": list(ingredient_keys),
# "Encapsulating radius": list(ingredient_radii.values()),
# "Average number packed": list(avg_num_packed.values())
# })
md_object.add_table(header="Ingredient Analysis", table=pd.DataFrame([text_list]))

# TODO: check if this is needed
# path to save report and other outputs
if output_image_location is None:
output_image_location = self.output_path
Expand All @@ -509,6 +545,7 @@ def create_report(
packing_results_path = self.packing_results_path
figure_path = packing_results_path / "figures"

# add packing image to report
md_object.add_images(
header="Packing image",
image_text=["Packing image"],
Expand Down

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