Initial commit

4 files changed, 459 insertions, 0 deletions

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..e98fe38
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,38 @@
+CC = gcc
+CFLAGS += -g -Wall -O3
+CPPFLAGS += -MMD
+LDFLAGS += -pthread -lm
+
+PP_BOLD := $(shell tput bold)
+PP_RESET := $(shell tput sgr0)
+PP_CC := $(PP_BOLD)$(shell tput setf 6)CC$(PP_RESET)
+PP_LD := $(PP_BOLD)$(shell tput setf 2)LD$(PP_RESET)
+PP_RM := $(PP_BOLD)$(shell tput setf 4)RM$(PP_RESET)
+
+SRC := src/e2e.c \
+       src/main.c
+       
+OBJ := $(SRC:src/%.c=obj/%.o)
+OUT := e2e
+
+all: $(OUT)
+
+-include $(OBJ:.o=.d)
+
+obj/%.o : src/%.c
+	@echo "$(PP_CC) src/$*.c"
+	@mkdir -p $(@D)
+	@$(CC) $(CFLAGS) $(CPPFLAGS) -c src/$*.c -o obj/$*.o
+
+$(OUT): $(OBJ)
+	@echo "$(PP_LD) $(OUT)"
+	@$(CC) $(OBJ) -o $(OUT) $(LDFLAGS)
+
+clean:
+	@echo "${PP_RM} obj"
+	@rm -rf obj
+	@echo "${PP_RM} ${OUT}"
+	@rm -rf ${OUT}
+
+.PHONY: clean
+
diff --git a/src/e2e.c b/src/e2e.c
new file mode 100644
index 0000000..1ab1449
--- /dev/null
+++ b/src/e2e.c
@@ -0,0 +1,363 @@
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+#include "e2e.h"
+
+uint32_t u32le(const char *src)
+{
+	uint8_t bytes[4];
+
+	memcpy(bytes, src, 4);
+
+	return (uint32_t)bytes[0]
+	       + (((uint32_t)bytes[1]) << 8)
+	       + (((uint32_t)bytes[2]) << 16)
+	       + (((uint32_t)bytes[3]) << 24);
+}
+
+static int make_pointer(const char *start, const char *end,
+                        const char *pos, const char **out)
+{
+	uint32_t ptroffs;
+
+	ptroffs = u32le(pos);
+
+	if (!ptroffs)
+		*out = NULL;
+	else {
+		if (ptroffs > end - start)
+			return 1;
+
+		*out = start + ptroffs;
+	}
+
+	return 0;
+}
+
+#define HEADER_END 36
+
+#define DIRECTORY_NUM_ENTRIES   36
+#define DIRECTORY_CURRENT       40
+#define DIRECTORY_NEXT          44
+#define DIRECTORY_END          52
+
+#define ENTRY_POS          0
+#define ENTRY_START        4 
+#define ENTRY_SIZE         8
+#define ENTRY_PATIENT_ID   16
+#define ENTRY_STUDY_ID     20
+#define ENTRY_SERIES_ID    24
+#define ENTRY_SLICE_ID     28
+#define ENTRY_TYPE         36
+#define ENTRY_END          44
+
+#define CHUNK_POS          20
+#define CHUNK_SIZE         24
+#define CHUNK_PATIENT_ID   32
+#define CHUNK_STUDY_ID     36
+#define CHUNK_SERIES_ID    40
+#define CHUNK_SLICE_ID     44
+#define CHUNK_IND          48
+#define CHUNK_TYPE         52
+#define CHUNK_HEADER_END   60
+
+#define DATA_IMAGE  0x40000000
+
+#define IMAGE_SIZE      0
+#define IMAGE_TYPE      4
+#define IMAGE_WIDTH     12
+#define IMAGE_HEIGHT    16
+#define IMAGE_IMAGE     20
+
+#define IMAGE_FUNDUS    0x02010201
+#define IMAGE_TOMOGRAM  0x02200201
+
+#define UF16_MANTISSA_MASK  ((1 << 11) - 1)  // 10 most significant bits
+
+struct e2e_directory {
+	size_t num_entries;
+	const char *current, *next;
+};
+
+struct e2e_entry {
+	const char *start;
+	size_t size;
+
+	uint32_t patient_id, study_id, series_id, slice_id, type;
+};
+
+struct e2e_chunk {
+	const char *origin;
+	const struct e2e_entry *entry;
+
+	size_t size;
+	uint32_t patient_id, study_id, series_id, slice_id, type;
+};
+
+struct e2e_fundus {
+	size_t size, width, height;
+
+	uint32_t type;
+
+};
+
+static int read_fundus(const char *start, const char *end, const char *cursor,
+                       size_t width, size_t height)
+{
+	FILE *fp;
+	char buffer[1024];
+
+	snprintf(buffer, sizeof(buffer), "out/fundus_%tx.py", cursor - start);
+	fp = fopen(buffer, "w");
+
+	fprintf(fp, "data = [\n");
+	for (size_t y = 0; y < height; y++) {
+		fprintf(fp, "\t[");
+
+		for (size_t x = 0; x < width; x++) {
+			uint8_t px;
+
+			memcpy(&px, cursor + y * width + x, 1);
+			fprintf(fp, "%s% 3hhu", x ? ", " : "", px);
+		}
+		fprintf(fp, "]%s\n", y + 1 >= height ? "" : ",");
+	}
+	fprintf(fp, "]\n");
+
+	fclose(fp);
+	return 0;
+}
+
+static int read_tomogram(const char *start, const char *end, const char *cursor,
+                       size_t width, size_t height)
+{
+	FILE *fp;
+	char buffer[1024];
+
+	snprintf(buffer, sizeof(buffer), "out/tomogram_%tx.py", cursor - start);
+	fp = fopen(buffer, "w");
+
+	fprintf(fp, "data = [\n");
+	for (size_t y = 0; y < height; y++) {
+		fprintf(fp, "\t[");
+
+		for (size_t x = 0; x < width; x++) {
+			uint16_t raw;
+			int exp, man;
+			float px;
+
+			memcpy(&raw, cursor + (y * width + x) * 2, 2);
+
+			man = raw & UF16_MANTISSA_MASK;
+			exp = (raw & ~UF16_MANTISSA_MASK) >> 10;
+
+			px = man * exp2f(exp);
+			fprintf(fp, "%s%e", x ? ", " : "", px);
+		}
+		fprintf(fp, "]%s\n", y + 1 >= height ? "" : ",");
+	}
+	fprintf(fp, "]\n");
+
+	fclose(fp);
+	return 0;
+}
+
+static int read_image(const char *start, const char *end,
+                      const struct e2e_chunk *chunk)
+{
+	const char *cursor = chunk->origin + CHUNK_HEADER_END;
+	size_t size, width, height;
+	uint32_t type;
+
+	if (cursor + IMAGE_IMAGE > end) {
+		fprintf(stderr, "Image data at %td ends past the end of file.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	size = u32le(cursor + IMAGE_SIZE);
+	type = u32le(cursor + IMAGE_TYPE);
+	width = u32le(cursor + IMAGE_WIDTH);
+	height = u32le(cursor + IMAGE_HEIGHT);
+
+	printf("# %08tx       Image data: %zux%zu, size=%zu\n",
+	       cursor - start, width, height, size);
+	printf("# Slice is %d\n", chunk->slice_id);
+	printf("# Type is %08x\n", type);
+
+	switch (type) {
+	case IMAGE_FUNDUS:
+		read_fundus(start, end, cursor + IMAGE_IMAGE, width, height);
+		break;
+
+	case IMAGE_TOMOGRAM:
+		read_tomogram(start, end, cursor + IMAGE_IMAGE, width, height);
+		break;
+	}
+
+	return 0;
+}
+
+static int read_chunk(const char *start, const char *end,
+                      const struct e2e_entry *entry, struct e2e_chunk *chunk)
+{
+	const char *cursor = entry->start, *pos;
+
+	chunk->entry = entry;
+	chunk->origin = cursor;
+
+	if (cursor + CHUNK_HEADER_END > end) {
+		fprintf(stderr, "Chunk at %td ends past the end of file.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	if (make_pointer(start, end, cursor + CHUNK_POS, &pos)) {
+		fprintf(stderr, "Chunk at %td has a bad 'pos' entry.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	if (pos != cursor) {
+		fprintf(stderr, "Chunk at %td has a 'pos' entry that differs from the entry's actual position",
+		        cursor - start);
+		return 1;
+	}
+
+	chunk->size = u32le(cursor + CHUNK_SIZE);
+	chunk->patient_id = u32le(cursor + CHUNK_PATIENT_ID);
+	chunk->study_id = u32le(cursor + CHUNK_STUDY_ID);
+	chunk->series_id = u32le(cursor + CHUNK_SERIES_ID);
+	chunk->slice_id = u32le(cursor + CHUNK_SLICE_ID);
+	chunk->type = u32le(cursor + CHUNK_TYPE);
+
+	return 0;
+}
+
+static int read_entry(const char *start, const char *end,
+                      const char *cursor, struct e2e_entry *entry)
+{
+	const char *pos;
+
+	if (cursor + ENTRY_END > end) {
+		fprintf(stderr, "Entry at %td ends past the end of file.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	if (make_pointer(start, end, cursor + ENTRY_POS, &pos)) {
+		fprintf(stderr, "Entry at %td has a bad 'pos' entry.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	if (pos != cursor) {
+		fprintf(stderr, "Entry at %td has a 'pos' entry that differs from the entry's actual position",
+		        cursor - start);
+		return 1;
+	}
+
+	if (make_pointer(start, end, cursor + ENTRY_START, &entry->start)) {
+		fprintf(stderr, "Entry at %td has a bad 'start' entry.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	entry->size = u32le(cursor + ENTRY_SIZE);
+	entry->patient_id = u32le(cursor + ENTRY_PATIENT_ID);
+	entry->study_id = u32le(cursor + ENTRY_STUDY_ID);
+	entry->series_id = u32le(cursor + ENTRY_SERIES_ID);
+	entry->slice_id = u32le(cursor + ENTRY_SLICE_ID);
+	entry->type = u32le(cursor + ENTRY_TYPE);
+
+	return 0;
+}
+
+static int read_directory(const char *start, const char *end,
+                          const char *cursor, struct e2e_directory *dir)
+{
+	if (cursor + DIRECTORY_END > end) {
+		fprintf(stderr, "Directory at %td ends past the end of file.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	dir->num_entries = u32le(cursor + DIRECTORY_NUM_ENTRIES);
+
+	if (make_pointer(start, end, cursor + DIRECTORY_CURRENT, &dir->current))  {
+		fprintf(stderr, "Directory at %td contains a bad 'current' field.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	if (make_pointer(start, end, cursor + DIRECTORY_NEXT, &dir->next))  {
+		fprintf(stderr, "Directory at %td contains a bad 'current' field.\n",
+		        cursor - start);
+		return 1;
+	}
+
+	return 0;
+}
+
+int e2e_read(const char *start, const char *end)
+{
+	int rv;
+	const char *cursor;
+
+	if (start + HEADER_END > end) {
+		fprintf(stderr, "File too short to be an E2E file.\n");
+		return 1;
+	}
+
+	// TODO: verify the header
+
+	cursor = start + HEADER_END;
+	cursor += DIRECTORY_END; // skip the first directory (wtf?)
+
+	while (cursor) {
+		struct e2e_directory dir;
+
+		rv = read_directory(start, end, cursor, &dir);
+		if (rv)
+			return rv;
+
+		printf("# %08tx Directory: num_entries=%zu, current=%08td, next=%td\n",
+		       cursor - start, dir.num_entries, dir.current - start,
+		       dir.next ? dir.next - start : 0);
+
+		for (size_t i = 0; i < dir.num_entries; i++) {
+			const char *entry_cursor;
+			struct e2e_entry entry;
+			struct e2e_chunk chunk;
+
+			entry_cursor = cursor + DIRECTORY_END + i * ENTRY_END;
+			rv = read_entry(start, end, entry_cursor, &entry);
+			if (rv)
+				return rv;
+
+			printf("# %08tx   Entry %zu: start=%08tx\n",
+			       entry_cursor - start, i,
+			       entry.start ? entry.start - start : 0);
+
+			if (!entry.start)
+				continue;
+
+			rv = read_chunk(start, end, &entry, &chunk);
+			if (rv)
+				continue;
+
+			printf("# %08tx     Chunk, size=%zu, type=%08x\n",
+			       entry.start - start, chunk.size, chunk.type);
+
+			switch (chunk.type) {
+			case DATA_IMAGE:
+				read_image(start, end, &chunk);
+				break;
+			}
+		}
+
+		cursor = dir.next;
+	}
+
+	return 0;
+}
\ No newline at end of file
diff --git a/src/e2e.h b/src/e2e.h
new file mode 100644
index 0000000..d7f7a13
--- /dev/null
+++ b/src/e2e.h
@@ -0,0 +1,3 @@
+#include <inttypes.h>
+
+int e2e_read(const char *start, const char *end);
\ No newline at end of file
diff --git a/src/main.c b/src/main.c
new file mode 100644
index 0000000..e51d863
--- /dev/null
+++ b/src/main.c
@@ -0,0 +1,55 @@
+#include <stdlib.h>
+#include <inttypes.h>
+#include <stdio.h>
+#include <errno.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <sys/mman.h>
+
+#include "e2e.h"
+
+uint32_t u32le(const char*);
+
+int main(int argc, char **argv)
+{
+	int rv = 0;
+	char *inpath;
+	int fd;
+	struct stat st;
+	void *input;
+
+	if (argc < 2) {
+		fprintf(stderr, "%s [FILE]\n", argv[0]);
+		return 1;
+	}
+
+	inpath = argv[1];
+
+	fd = open(inpath, O_RDONLY);
+	if (fd == -1) {
+		perror("open");
+		return 1;
+	}
+
+	if (fstat(fd, &st) == -1) {
+		perror("fstat");
+		rv = 1;
+		goto error_mmap;
+	}
+
+	input = mmap(NULL, st.st_size, PROT_READ, MAP_PRIVATE, fd, 0);
+	if (!input) {
+		perror("mmap");
+		rv = 1;
+		goto error_mmap;
+	}
+
+	e2e_read(input, input + st.st_size);
+
+	munmap(input, st.st_size);
+error_mmap:
+	close(fd);
+	return rv;
+}
\ No newline at end of file